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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3fkq ATP NtrC-like two-domain protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3fkq ATPNtrC-like two-domain protein / 0.928
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.785
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.766
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.757
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.757
4idn GNPAtlastin-1 3.6.5 0.755
4v02 ATPSite-determining protein / 0.755
4ohv ANPProtein clpf-1 / 0.750
5jlj GNPGTP-binding nuclear protein Ran / 0.750
3q9l ATPSeptum site-determining protein MinD / 0.749
5aun ADPIron-sulfur cluster carrier protein / 0.746
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.745
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.745
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.744
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
3oes GNPGTPase RhebL1 / 0.743
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.741
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.741
2hld ANPATP synthase subunit alpha, mitochondrial / 0.740
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.740
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.740
4g0n GNPGTPase HRas / 0.739
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.738
5dha GNPGTP-binding nuclear protein Ran / 0.738
5di3 GNPADP-ribosylation factor-like protein 3 / 0.737
4idp GNPAtlastin-1 3.6.5 0.732
3tgp GNPGTPase HRas / 0.731
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.729
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.729
2c5l GTPGTPase HRas / 0.729
4xvq GNPGTPase HRas / 0.729
1okk GCPSignal recognition particle protein / 0.728
1okk GCPSignal recognition particle receptor FtsY / 0.728
1z2c GNPRho-related GTP-binding protein RhoC / 0.727
4rz3 ADPSite-determining protein / 0.727
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.726
3k9l GNPGTPase HRas / 0.725
2r9v ATPATP synthase subunit alpha / 0.724
2j7p GNPSignal recognition particle protein / 0.723
2j7p GNPSignal recognition particle receptor FtsY / 0.723
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.723
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.722
4goj GNPADP-ribosylation factor-like protein 3 / 0.721
4gp6 ADPMetallophosphoesterase / 0.721
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.719
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.719
1kmq GNPTransforming protein RhoA / 0.719
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.719
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.719
3pit GNPRas-related protein M-Ras / 0.719
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.718
3lbn GNPGTPase HRas / 0.718
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.717
1ky2 GNPGTP-binding protein YPT7 / 0.717
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.717
3kko GNPRas-related protein M-Ras / 0.717
3oiw GNPGTPase HRas / 0.717
4dlv GNPGTPase HRas / 0.717
2ffq GSPRas-related protein Rab-6B / 0.716
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.716
3l8y GNPGTPase HRas / 0.716
2rgc GNPGTPase HRas / 0.715
3rab GNPRas-related protein Rab-3A / 0.715
4ihq ADPConserved Archaeal protein / 0.715
4l9w GNPGTPase HRas / 0.715
5l3s GNPSignal recognition particle receptor FtsY / 0.714
1yu9 GNPRas-related protein Rab-4A / 0.713
2bc9 GNPGuanylate-binding protein 1 / 0.713
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.712
4lhv GDPRas-related protein Rab-8A / 0.712
4xvr GNPGTPase HRas / 0.712
1uad GNPRas-related protein Ral-A / 0.711
3b1x GNPFerrous iron transport protein B / 0.711
3vhx GTPADP-ribosylation factor 6 / 0.710
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.710
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.709
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.709
3zia ATPATP synthase subunit alpha, mitochondrial / 0.709
4jjz ADPFormate--tetrahydrofolate ligase / 0.709
5cyo GDPSeptin-9 / 0.709
1vg8 GNPRas-related protein Rab-7a / 0.708
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.708
4yqf GDPSeptin-9 / 0.708
1wdt GTPElongation factor G (EF-G-2) / 0.707
1zc3 GNPRas-related protein Ral-A / 0.707
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.707
2cl6 CAGGTPase HRas / 0.707
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.707
4dlz GNPGTPase HRas / 0.707
4iok ADPFormate--tetrahydrofolate ligase / 0.707
3x1z GNPRas-related protein Rap-1b / 0.706
2bku GTPGTP-binding nuclear protein Ran / 0.705
3oiv GNPGTPase HRas / 0.705
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.704
1rj9 GCPSignal recognition particle receptor FtsY / 0.704
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.704
3bc1 GNPRas-related protein Rab-27A / 0.704
3qbt GNPRas-related protein Rab-8A / 0.704
4d0l GSPRas-related protein Rab-11A / 0.704
4jsy GTPMetallophosphoesterase / 0.704
4l8g GDPGTPase KRas / 0.704
4qxa GTPRas-related protein Rab-9A / 0.704
5c46 GSPRas-related protein Rab-11A / 0.704
2gcp GSPRho-related GTP-binding protein RhoC / 0.703
2rge GNPGTPase HRas / 0.703
3r9x GNPGTPase Era / 0.703
4obe GDPGTPase KRas / 0.703
2jlr ANPGenome polyprotein 3.4.21.91 0.702
2rgb GNPGTPase HRas / 0.702
3k8y GNPGTPase HRas / 0.702
3rs7 GNPGTPase HRas / 0.702
3rsl GNPGTPase HRas / 0.702
4dlt GNPGTPase HRas / 0.702
4l9s GDPGTPase HRas / 0.702
3oiu GNPGTPase HRas / 0.701
3tkl GTPRas-related protein Rab-1A / 0.701
4cid ANPEH domain-containing protein 2 / 0.701
4dls GNPGTPase HRas / 0.701
4dsn GCPGTPase KRas / 0.701
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.701
1w5t ANPORC1-type DNA replication protein 2 / 0.700
2l0x GDPGTP-binding protein Rheb / 0.700
3i3s GNPGTPase HRas / 0.700
3v4f GNPGTPase HRas / 0.700
4dlw GNPGTPase HRas / 0.700
4dlx GNPGTPase HRas / 0.700
2bme GNPRas-related protein Rab-4A / 0.699
1tu3 GNPRas-related protein Rab-5A / 0.698
2fg5 GNPRas-related protein Rab-31 / 0.698
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.698
3ftq GNPSeptin-2 / 0.698
4qm6 GTPMetallophosphoesterase / 0.698
1g17 GNPRas-related protein SEC4 / 0.697
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.697
4hdq GNPRas-related protein Rap-1b / 0.697
1wbb ADPDNA mismatch repair protein MutS / 0.696
4lhw GNPRas-related protein Rab-8A / 0.696
4z54 GDPNeuronal-specific septin-3 / 0.696
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.695
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.695
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.694
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.694
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.694
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.694
2zts ADPUncharacterized protein / 0.694
3kb1 ADPIron-sulfur cluster carrier protein / 0.694
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.694
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.694
5bn3 ADPV-type ATP synthase alpha chain / 0.694
5bn3 ADPNEQ263 / 0.694
3tso GNPRas-related protein Rab-25 / 0.693
5dif GNPGTP-binding nuclear protein Ran / 0.693
1mmg AGSMyosin-2 heavy chain / 0.692
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.692
2q3f GNPRas-related GTP-binding protein D / 0.692
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.692
4g01 GDPRas-related protein RABF2b / 0.692
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.692
4ylg GDPADP-ribosylation factor 1, putative / 0.691
5k5z ANPUncharacterized protein / 0.691
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.690
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.690
4y0v GDPADP-ribosylation factor 1, putative / 0.690
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.689
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
3c41 ANPAmino acid ABC transporter / 0.689
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.689
3tnf GNPRas-related protein Rab-8A / 0.689
4qbg AP5Adenylate kinase / 0.689
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.689
1xmv ADPProtein RecA / 0.688
4ap0 ADPKinesin-like protein KIF11 / 0.688
4asu ADPATP synthase subunit alpha, mitochondrial / 0.688
4luc GDPGTPase KRas / 0.688
2ql6 ADPNicotinamide riboside kinase 1 / 0.687
2rgg GNPGTPase HRas / 0.687
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.687
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.686
1zc4 GNPRas-related protein Ral-A / 0.686
3a6p GTPGTP-binding nuclear protein Ran / 0.686
3tjz GNPADP-ribosylation factor 1 / 0.686
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.686
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.686
4c30 ANPDNA helicase / 0.686
4cf7 ADPAdenylate kinase / 0.686
2qen ADPWalker-Type ATPase / 0.685
4ldj GDPGTPase KRas / 0.685
5b2z GNPGTPase HRas / 0.685
1l8q ADPChromosomal replication initiator protein DnaA / 0.684
1zio AP5Adenylate kinase / 0.684
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.684
2uyi ADPKinesin-like protein KIF11 / 0.684
3ddc GNPGTPase HRas / 0.684
4lv6 GDPGTPase KRas / 0.684
4ohw ATPProtein clpf-1 / 0.684
4uj3 GNPRas-related protein Rab-11A / 0.684
5ftc ADPTPR domain protein / 0.684
3q5d GDPAtlastin-1 3.6.5 0.683
4kvg GTPRas-related protein Rap-1A / 0.683
4js0 GNPCell division control protein 42 homolog / 0.682
1gwn GTPRho-related GTP-binding protein RhoE / 0.681
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
1yra GDPGPN-loop GTPase PAB0955 / 0.681
2ce2 GDPGTPase HRas / 0.681
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.681
3cob ADPKinesin heavy chain-like protein / 0.681
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.681
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.681
4xsg GSPTransforming protein RhoA / 0.681
1jx2 ADPMyosin-2 heavy chain / 0.680
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.680
3eg5 GNPCell division control protein 42 homolog / 0.680
4dzz ADPPlasmid partitioning protein ParF / 0.680
4qos ADPPsp operon transcriptional activator / 0.680
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.680
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.679
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.679
4pjk ADPMyosin-2 heavy chain / 0.679
4x8o AP5Adenylate kinase / 0.679
5hpy GDPTransforming protein RhoA / 0.679
3myk ANPMyosin-2 heavy chain / 0.678
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.678
4nh0 ATPESX secretion system protein EccC / 0.678
1x1r GDPRas-related protein M-Ras / 0.677
1yzq GNPRas-related protein Rab-6A / 0.677
2fe4 GDPRas-related protein Rab-6B / 0.677
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.677
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.677
4pfp ADPUnconventional myosin-VI / 0.677
4xoi GTPTransforming protein RhoA / 0.677
5fl3 ADPPili retraction protein PilT / 0.677
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.676
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
1oix GDPRas-related protein Rab-11A / 0.676
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.676
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.676
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.676
3lbh GNPGTPase HRas / 0.676
3r9i ADPSeptum site-determining protein MinD / 0.676
4oi2 ADPProtein clpf-1 / 0.676
1ibr GNPGTP-binding nuclear protein Ran / 0.675
2fna ADPUncharacterized protein / 0.675
4db1 ANPMyosin-7 / 0.675
4hdo GNPRas-related protein Rap-1b / 0.675
4pjj ADPUnconventional myosin-VI / 0.675
1z2a GDPRas-related protein Rab-23 / 0.674
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.674
2y65 ADPKinesin heavy chain / 0.674
3a58 GNPGTP-binding protein RHO1 / 0.674
4jl5 ADPAdenylate kinase / 0.674
1z0d GDPRas-related protein Rab-5C / 0.673
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.673
4jl6 ADPAdenylate kinase / 0.673
4jlo ADPAdenylate kinase / 0.673
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.672
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.672
2iut AGSDNA translocase FtsK / 0.672
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.672
3jvv ACPTwitching mobility protein / 0.672
4cym GCPRas-related protein Rab-32 / 0.672
4tyq AP5Adenylate kinase / 0.672
2c98 ADPPsp operon transcriptional activator / 0.671
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.671
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.671
4ike ADPAdenylate kinase / 0.671
4jky ADPAdenylate kinase / 0.671
4nyi GNPGTPase HRas / 0.671
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.670
2pg2 ADPKinesin-like protein KIF11 / 0.670
3k3b ADPKinesin-like protein KIF11 / 0.670
3mjh GTPRas-related protein Rab-5A / 0.670
3w3z GTPGTP-binding nuclear protein Ran / 0.670
4jld ADPAdenylate kinase / 0.670
1sdm ADPKinesin heavy chain-like protein / 0.669
1xms ANPProtein RecA / 0.669
2x2r ADPKinesin-like protein KIF11 / 0.669
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.669
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
1sq5 ADPPantothenate kinase 2.7.1.33 0.668
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.668
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
2x7e ADPKinesin-like protein KIF11 / 0.668
3rs0 GNPGTPase HRas / 0.668
4nyj GNPGTPase HRas / 0.668
4q03 GDPGTPase KRas / 0.668
4tq9 GDPGTPase KRas / 0.668
4uj5 GNPRas-related protein Rab-11A / 0.668
5d3q GDPDynamin-1 3.6.5.5 0.668
1ow3 GDPTransforming protein RhoA / 0.667
1yrs ADPKinesin-like protein KIF11 / 0.667
2zfi ADPKinesin-like protein KIF1A / 0.667
1cxz GSPTransforming protein RhoA / 0.666
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.666
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.666
1f5n GNPGuanylate-binding protein 1 / 0.665
1lfd GNPGTPase HRas / 0.665
1p9w ANPType II secretion system protein E / 0.665
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.665
4rkf GNPRas-related protein Rab-3 / 0.665
1m7b GTPRho-related GTP-binding protein RhoE / 0.664
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.664
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
3oee ANPATP synthase subunit alpha, mitochondrial / 0.664
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
4k81 GTPGTPase HRas / 0.664
1n6l GTPRas-related protein Rab-5A / 0.663
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.663
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.663
4lrw GDPGTPase KRas / 0.663
1ake AP5Adenylate kinase / 0.662
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.662
3x1w GDPRas-related protein Rap-1b / 0.662
2gm1 ADPKinesin-like protein KIF11 / 0.661
4ql3 GDPGTPase KRas / 0.661
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.660
1xtr GNPGTP-binding protein Rheb / 0.660
3ea5 GDPGTP-binding nuclear protein Ran / 0.660
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.660
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.660
4dso GSPGTPase KRas / 0.659
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
4ohx ADPProtein clpf-1 / 0.659
4lpk GDPGTPase KRas / 0.658
4pk4 ADPUnconventional myosin-VI / 0.658
1b7t ADPMyosin heavy chain, striated muscle / 0.657
3d8b ADPFidgetin-like protein 1 3.6.4 0.657
5cyp GSPSeptin-9 / 0.657
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.656
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.656
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
4a1z ADPKinesin-like protein KIF11 / 0.656
1fnn ADPORC1-type DNA replication protein / 0.655
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.655
3tqc ADPPantothenate kinase / 0.655
4hi0 GDPUrease accessory protein UreG / 0.655
2bbw GP5Adenylate kinase 4, mitochondrial / 0.654
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.654
3hqd ANPKinesin-like protein KIF11 / 0.653
3lbi GNPGTPase HRas / 0.653
4a28 ADPKinesin-like protein KIF11 / 0.653
1d5c GDPGTPase (Rab6) / 0.652
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.652
3rs5 GNPGTPase HRas / 0.652
4epw GDPGTPase KRas / 0.652
3cph GDPRas-related protein SEC4 / 0.651
3rs4 GNPGTPase HRas / 0.651
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.651
3kuc GDPRas-related protein Rap-1A / 0.650
3law GNPRas-related protein Rab-7a / 0.650
3tlx ADPAdenylate kinase 2 / 0.650
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.650