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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
1xms ANP Protein RecA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1xms ANPProtein RecA / 0.986
1xmv ADPProtein RecA / 0.794
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.767
2ffq GSPRas-related protein Rab-6B / 0.762
3oes GNPGTPase RhebL1 / 0.757
3rab GNPRas-related protein Rab-3A / 0.757
1ky2 GNPGTP-binding protein YPT7 / 0.755
1yzq GNPRas-related protein Rab-6A / 0.754
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.754
4asu ADPATP synthase subunit alpha, mitochondrial / 0.753
4idn GNPAtlastin-1 3.6.5 0.751
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.750
4idp GNPAtlastin-1 3.6.5 0.747
1xtr GNPGTP-binding protein Rheb / 0.743
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.742
2rgg GNPGTPase HRas / 0.742
2rgb GNPGTPase HRas / 0.741
2rge GNPGTPase HRas / 0.741
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.741
4qxa GTPRas-related protein Rab-9A / 0.741
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.740
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.740
1uad GNPRas-related protein Ral-A / 0.739
1zc3 GNPRas-related protein Ral-A / 0.739
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.739
2rgc GNPGTPase HRas / 0.739
3ddc GNPGTPase HRas / 0.739
3kko GNPRas-related protein M-Ras / 0.739
3mjh GTPRas-related protein Rab-5A / 0.739
4hdq GNPRas-related protein Rap-1b / 0.739
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.738
3i3s GNPGTPase HRas / 0.738
3k8y GNPGTPase HRas / 0.738
3lbi GNPGTPase HRas / 0.738
3oiu GNPGTPase HRas / 0.738
3oiv GNPGTPase HRas / 0.738
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.738
4dls GNPGTPase HRas / 0.738
4dlt GNPGTPase HRas / 0.738
4dlv GNPGTPase HRas / 0.738
3rs0 GNPGTPase HRas / 0.737
3rs4 GNPGTPase HRas / 0.737
3rs5 GNPGTPase HRas / 0.737
3rs7 GNPGTPase HRas / 0.737
3rsl GNPGTPase HRas / 0.737
3v4f GNPGTPase HRas / 0.737
4dlx GNPGTPase HRas / 0.737
2bme GNPRas-related protein Rab-4A / 0.736
2fna ADPUncharacterized protein / 0.736
2jlr ANPGenome polyprotein 3.4.21.91 0.736
3l8y GNPGTPase HRas / 0.736
3oiw GNPGTPase HRas / 0.736
4dlw GNPGTPase HRas / 0.736
4dlz GNPGTPase HRas / 0.736
4xvq GNPGTPase HRas / 0.736
5b2z GNPGTPase HRas / 0.736
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.735
3k9l GNPGTPase HRas / 0.735
3lbn GNPGTPase HRas / 0.735
2zts ADPUncharacterized protein / 0.733
4yqf GDPSeptin-9 / 0.733
4jjz ADPFormate--tetrahydrofolate ligase / 0.729
3c41 ANPAmino acid ABC transporter / 0.728
5dif GNPGTP-binding nuclear protein Ran / 0.728
2x2r ADPKinesin-like protein KIF11 / 0.727
5di3 GNPADP-ribosylation factor-like protein 3 / 0.727
2pg2 ADPKinesin-like protein KIF11 / 0.726
2uyi ADPKinesin-like protein KIF11 / 0.726
4xsg GSPTransforming protein RhoA / 0.726
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.725
3ftq GNPSeptin-2 / 0.725
4gp6 ADPMetallophosphoesterase / 0.725
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.723
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.722
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.722
2xae ADPKinesin-like protein KIF11 / 0.722
3tgp GNPGTPase HRas / 0.722
4rkf GNPRas-related protein Rab-3 / 0.722
1n6l GTPRas-related protein Rab-5A / 0.721
1z2a GDPRas-related protein Rab-23 / 0.721
5cyo GDPSeptin-9 / 0.721
2c5l GTPGTPase HRas / 0.720
5jlj GNPGTP-binding nuclear protein Ran / 0.720
1f5n GNPGuanylate-binding protein 1 / 0.719
3q5d GDPAtlastin-1 3.6.5 0.719
3x1z GNPRas-related protein Rap-1b / 0.719
4dsu GDPGTPase KRas / 0.719
4nyj GNPGTPase HRas / 0.719
1z0d GDPRas-related protein Rab-5C / 0.718
2j5x GSPADP-ribosylation factor 6 / 0.718
4dzz ADPPlasmid partitioning protein ParF / 0.718
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.717
3zfd ANPChromosome-associated kinesin KIF4 / 0.716
3myk ANPMyosin-2 heavy chain / 0.715
4ihq ADPConserved Archaeal protein / 0.714
2q3f GNPRas-related GTP-binding protein D / 0.713
4dsn GCPGTPase KRas / 0.713
5aun ADPIron-sulfur cluster carrier protein / 0.713
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.712
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.712
2bc9 GNPGuanylate-binding protein 1 / 0.712
4zca ADPKinesin-like protein KIF11 / 0.712
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.711
1mma ADPMyosin-2 heavy chain / 0.711
4ohv ANPProtein clpf-1 / 0.711
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.711
2cl6 CAGGTPase HRas / 0.710
1lfd GNPGTPase HRas / 0.709
2x7e ADPKinesin-like protein KIF11 / 0.709
1vg8 GNPRas-related protein Rab-7a / 0.708
3law GNPRas-related protein Rab-7a / 0.708
3lbh GNPGTPase HRas / 0.708
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.708
1fnn ADPORC1-type DNA replication protein / 0.707
1w5t ANPORC1-type DNA replication protein 2 / 0.707
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.707
3pit GNPRas-related protein M-Ras / 0.707
1kmq GNPTransforming protein RhoA / 0.706
2fe4 GDPRas-related protein Rab-6B / 0.706
2y65 ADPKinesin heavy chain / 0.706
4js0 GNPCell division control protein 42 homolog / 0.706
1v8k ANPKinesin-like protein KIF2C / 0.705
4db1 ANPMyosin-7 / 0.705
4dxa GSPRas-related protein Rap-1b / 0.705
4hdo GNPRas-related protein Rap-1b / 0.705
4kvg GTPRas-related protein Rap-1A / 0.705
4lrw GDPGTPase KRas / 0.705
4z54 GDPNeuronal-specific septin-3 / 0.705
5fl3 ADPPili retraction protein PilT / 0.705
5k5z ANPUncharacterized protein / 0.705
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.704
2zrj AGSProtein RecA / 0.704
3q9l ATPSeptum site-determining protein MinD / 0.704
4goj GNPADP-ribosylation factor-like protein 3 / 0.704
4l8g GDPGTPase KRas / 0.704
4l9w GNPGTPase HRas / 0.704
4lhw GNPRas-related protein Rab-8A / 0.704
4y0v GDPADP-ribosylation factor 1, putative / 0.704
4ylg GDPADP-ribosylation factor 1, putative / 0.704
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.704
1yu9 GNPRas-related protein Rab-4A / 0.703
1zc4 GNPRas-related protein Ral-A / 0.703
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.702
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.702
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
2bku GTPGTP-binding nuclear protein Ran / 0.702
4epw GDPGTPase KRas / 0.702
4itr GDPCell division control protein 42 homolog / 0.702
4obe GDPGTPase KRas / 0.702
1z0f GDPRas-related protein Rab-14 / 0.701
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.701
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
3kkq GDPRas-related protein M-Ras / 0.701
5ftc ADPTPR domain protein / 0.701
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.700
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.700
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.700
2gm1 ADPKinesin-like protein KIF11 / 0.700
4cym GCPRas-related protein Rab-32 / 0.700
4l9s GDPGTPase HRas / 0.700
1jx2 ADPMyosin-2 heavy chain / 0.699
1x1r GDPRas-related protein M-Ras / 0.699
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.699
4lv6 GDPGTPase KRas / 0.699
4q02 GDPGTPase KRas / 0.699
4ql3 GDPGTPase KRas / 0.699
4tq9 GDPGTPase KRas / 0.699
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.698
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
1p9w ANPType II secretion system protein E / 0.698
1z2c GNPRho-related GTP-binding protein RhoC / 0.698
2dpx GDPGTP-binding protein RAD / 0.698
3kud GDPGTPase HRas / 0.698
3x1w GDPRas-related protein Rap-1b / 0.698
4epx GDPGTPase KRas / 0.698
4ldj GDPGTPase KRas / 0.698
4q03 GDPGTPase KRas / 0.698
4xvr GNPGTPase HRas / 0.698
1xp8 AGSProtein RecA / 0.697
2ce2 GDPGTPase HRas / 0.697
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.697
4jsy GTPMetallophosphoesterase / 0.697
4wa7 GDPGTPase KRas / 0.697
3thy ADPDNA mismatch repair protein Msh2 / 0.696
4g0n GNPGTPase HRas / 0.696
1ank ANPAdenylate kinase / 0.695
4nh0 ATPESX secretion system protein EccC / 0.695
4pjk ADPMyosin-2 heavy chain / 0.695
3kuc GDPRas-related protein Rap-1A / 0.694
4o2l GTPGTP-binding protein Rheb / 0.694
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.693
4pjj ADPUnconventional myosin-VI / 0.693
3tso GNPRas-related protein Rab-25 / 0.692
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.692
1g17 GNPRas-related protein SEC4 / 0.691
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.691
1yrs ADPKinesin-like protein KIF11 / 0.690
1rj9 GCPSignal recognition particle receptor FtsY / 0.689
1tu3 GNPRas-related protein Rab-5A / 0.689
2fg5 GNPRas-related protein Rab-31 / 0.689
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.689
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
3e5h GNPRas-related protein Rab-28 / 0.689
4iei ADPGene 2 protein / 0.689
4uj3 GNPRas-related protein Rab-11A / 0.689
1d5c GDPGTPase (Rab6) / 0.688
2zr9 DTPProtein RecA / 0.688
3qbt GNPRas-related protein Rab-8A / 0.688
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.688
1k5d GNPGTP-binding nuclear protein Ran / 0.687
3k1j ADPATP-dependent protease Lon / 0.686
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.686
1oix GDPRas-related protein Rab-11A / 0.685
2qen ADPWalker-Type ATPase / 0.685
4lpk GDPGTPase KRas / 0.685
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.684
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
1w5t ADPORC1-type DNA replication protein 2 / 0.684
4cf7 ADPAdenylate kinase / 0.684
2zro ADPProtein RecA / 0.683
3zia ATPATP synthase subunit alpha, mitochondrial / 0.683
4c2u ANPDNA helicase / 0.683
4nyi GNPGTPase HRas / 0.683
1ibr GNPGTP-binding nuclear protein Ran / 0.682
3ref GDPRho family GTPase / 0.682
4ohx ADPProtein clpf-1 / 0.682
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.681
1ii6 ADPKinesin-like protein KIF11 / 0.681
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.680
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.679
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.679
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.678
1rrg GDPADP-ribosylation factor 1 / 0.678
2hld ANPATP synthase subunit alpha, mitochondrial / 0.678
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.678
3cph GDPRas-related protein SEC4 / 0.678
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.678
4luc GDPGTPase KRas / 0.678
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.678
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.677
1nly AGSCag alpha / 0.677
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.676
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.675
1ake AP5Adenylate kinase / 0.672
1sdm ADPKinesin heavy chain-like protein / 0.672
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.672
3l9h ADPKinesin-like protein KIF11 / 0.672
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.671
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.671
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
3r9x GNPGTPase Era / 0.671
4g01 GDPRas-related protein RABF2b / 0.671
4oi2 ADPProtein clpf-1 / 0.671
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.671
1l8q ADPChromosomal replication initiator protein DnaA / 0.670
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.670
2zfi ADPKinesin-like protein KIF1A / 0.670
3tqc ADPPantothenate kinase / 0.670
2l0x GDPGTP-binding protein Rheb / 0.669
3cob ADPKinesin heavy chain-like protein / 0.669
3fkq ATPNtrC-like two-domain protein / 0.669
4ohw ATPProtein clpf-1 / 0.669
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.668
3k3b ADPKinesin-like protein KIF11 / 0.668
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.667
1ow3 GDPTransforming protein RhoA / 0.666
1w5s ADPORC1-type DNA replication protein 2 / 0.666
2iut AGSDNA translocase FtsK / 0.666
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.666
3tkl GTPRas-related protein Rab-1A / 0.666
4a28 ADPKinesin-like protein KIF11 / 0.666
4ap0 ADPKinesin-like protein KIF11 / 0.666
4iok ADPFormate--tetrahydrofolate ligase / 0.665
5dha GNPGTP-binding nuclear protein Ran / 0.665
1s1c GNPTransforming protein RhoA / 0.664
1yra GDPGPN-loop GTPase PAB0955 / 0.664
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.664
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.664
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.664
4ol0 GTPGTP-binding nuclear protein Ran / 0.664
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.663
1sxj ADPReplication factor C subunit 5 / 0.663
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.662
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.662
4hse ADPChaperone protein ClpB / 0.662
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.662
2ql6 ADPNicotinamide riboside kinase 1 / 0.661
4hi0 GDPUrease accessory protein UreG / 0.661
3jvv ACPTwitching mobility protein / 0.660
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.659
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
3ea5 GDPGTP-binding nuclear protein Ran / 0.659
3oee ANPATP synthase subunit alpha, mitochondrial / 0.659
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
3qi2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
4ag5 ADPType IV secretory pathway VirB4 components-like protein / 0.659
4b7b ADPKinesin-like protein KIF11 / 0.658
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.658
1z0a GDPRas-related protein Rab-2A / 0.657
2o8b ADPDNA mismatch repair protein Msh2 / 0.657
3tjz GNPADP-ribosylation factor 1 / 0.657
3sop GDPNeuronal-specific septin-3 / 0.656
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.656
1svl ADPLarge T antigen 3.6.4 0.655
3l1c ADPProtein claret segregational / 0.655
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.655
4ncl GDPEukaryotic translation initiation factor 5B / 0.655
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.654
2eck ADPAdenylate kinase / 0.654
3c16 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.654
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.654
4jl6 ADPAdenylate kinase / 0.654
1sq5 ADPPantothenate kinase 2.7.1.33 0.653
2fl2 ADPKinesin-like protein KIF11 / 0.653
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.653
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.652
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.652
4o2r GDPGTP-binding protein Rheb / 0.652
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.651
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.650
4e03 ADPPlasmid partitioning protein ParF / 0.650