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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
4c30 ANP DNA helicase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4c30 ANPDNA helicase / 1.124
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.843
4c2u ANPDNA helicase / 0.805
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.799
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.789
2rgx AP5Adenylate kinase / 0.785
3zfd ANPChromosome-associated kinesin KIF4 / 0.754
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.754
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.752
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.751
1mmg AGSMyosin-2 heavy chain / 0.736
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.731
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.731
4jlo ADPAdenylate kinase / 0.731
3rs4 GNPGTPase HRas / 0.730
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.729
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.729
4dlw GNPGTPase HRas / 0.729
2jlr ANPGenome polyprotein 3.4.21.91 0.726
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.725
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.724
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.722
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.720
4pfp ADPUnconventional myosin-VI / 0.719
2x7e ADPKinesin-like protein KIF11 / 0.718
3i3s GNPGTPase HRas / 0.718
4jsy GTPMetallophosphoesterase / 0.718
4mkf AP5Adenylate kinase / 0.718
4tyq AP5Adenylate kinase / 0.718
3rsl GNPGTPase HRas / 0.717
4jky ADPAdenylate kinase / 0.717
3oiu GNPGTPase HRas / 0.716
3rs0 GNPGTPase HRas / 0.716
3tso GNPRas-related protein Rab-25 / 0.716
4lhw GNPRas-related protein Rab-8A / 0.716
4pjk ADPMyosin-2 heavy chain / 0.716
5dif GNPGTP-binding nuclear protein Ran / 0.716
3l8y GNPGTPase HRas / 0.715
3pit GNPRas-related protein M-Ras / 0.715
3rs5 GNPGTPase HRas / 0.715
4g0n GNPGTPase HRas / 0.715
4jl5 ADPAdenylate kinase / 0.715
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.715
5b2z GNPGTPase HRas / 0.715
5bn3 ADPV-type ATP synthase alpha chain / 0.715
5bn3 ADPNEQ263 / 0.715
1ow3 GDPTransforming protein RhoA / 0.714
1fnn ADPORC1-type DNA replication protein / 0.713
3law GNPRas-related protein Rab-7a / 0.713
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.712
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.711
4jl6 ADPAdenylate kinase / 0.711
1w5s ADPORC1-type DNA replication protein 2 / 0.710
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
1w5t ADPORC1-type DNA replication protein 2 / 0.707
1p3j AP5Adenylate kinase / 0.706
4k81 GTPGTPase HRas / 0.706
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.705
3x1z GNPRas-related protein Rap-1b / 0.705
4l9w GNPGTPase HRas / 0.705
2cl6 CAGGTPase HRas / 0.704
3lbh GNPGTPase HRas / 0.704
3v4f GNPGTPase HRas / 0.704
4dlv GNPGTPase HRas / 0.704
4hdo GNPRas-related protein Rap-1b / 0.704
1zc3 GNPRas-related protein Ral-A / 0.703
3oiw GNPGTPase HRas / 0.703
4db1 ANPMyosin-7 / 0.703
4dlz GNPGTPase HRas / 0.703
4xvr GNPGTPase HRas / 0.703
2bme GNPRas-related protein Rab-4A / 0.702
2gm1 ADPKinesin-like protein KIF11 / 0.702
3lbi GNPGTPase HRas / 0.702
3lbn GNPGTPase HRas / 0.702
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.701
1yzq GNPRas-related protein Rab-6A / 0.701
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.701
3kko GNPRas-related protein M-Ras / 0.701
3vhx GTPADP-ribosylation factor 6 / 0.701
2rge GNPGTPase HRas / 0.700
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.700
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.700
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.699
2ffq GSPRas-related protein Rab-6B / 0.699
4dlx GNPGTPase HRas / 0.699
4jld ADPAdenylate kinase / 0.699
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.698
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
3rs7 GNPGTPase HRas / 0.698
4cym GCPRas-related protein Rab-32 / 0.698
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.698
3dl0 AP5Adenylate kinase / 0.697
1zc4 GNPRas-related protein Ral-A / 0.696
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.696
1f5n GNPGuanylate-binding protein 1 / 0.695
2rgc GNPGTPase HRas / 0.695
1fmw ATPMyosin-2 heavy chain / 0.694
1ake AP5Adenylate kinase / 0.693
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.693
3bc1 GNPRas-related protein Rab-27A / 0.692
3cob ADPKinesin heavy chain-like protein / 0.692
1n6l GTPRas-related protein Rab-5A / 0.691
1oe0 TTPDeoxynucleoside kinase / 0.691
2r9v ATPATP synthase subunit alpha / 0.690
3k8y GNPGTPase HRas / 0.690
3myk ANPMyosin-2 heavy chain / 0.690
3tgp GNPGTPase HRas / 0.690
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.689
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
2x2r ADPKinesin-like protein KIF11 / 0.689
2y65 ADPKinesin heavy chain / 0.689
4dlt GNPGTPase HRas / 0.689
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.689
3ddc GNPGTPase HRas / 0.688
4xvq GNPGTPase HRas / 0.688
1w5t ANPORC1-type DNA replication protein 2 / 0.687
3kuc GDPRas-related protein Rap-1A / 0.687
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.686
1kmq GNPTransforming protein RhoA / 0.686
3fkq ATPNtrC-like two-domain protein / 0.686
4ql3 GDPGTPase KRas / 0.686
4l9s GDPGTPase HRas / 0.685
4qxa GTPRas-related protein Rab-9A / 0.685
1jx2 ADPMyosin-2 heavy chain / 0.684
2uyi ADPKinesin-like protein KIF11 / 0.684
3b1x GNPFerrous iron transport protein B / 0.684
3oiv GNPGTPase HRas / 0.684
5l3s GNPSignal recognition particle receptor FtsY / 0.684
3eg5 GNPCell division control protein 42 homolog / 0.683
3q9l ATPSeptum site-determining protein MinD / 0.683
4gp6 ADPMetallophosphoesterase / 0.683
4idn GNPAtlastin-1 3.6.5 0.683
4ike ADPAdenylate kinase / 0.683
4qos ADPPsp operon transcriptional activator / 0.683
4uj3 GNPRas-related protein Rab-11A / 0.683
2fg5 GNPRas-related protein Rab-31 / 0.682
3dzd ADPTranscriptional regulator (NtrC family) / 0.682
4js0 GNPCell division control protein 42 homolog / 0.682
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.682
4uj5 GNPRas-related protein Rab-11A / 0.682
5aun ADPIron-sulfur cluster carrier protein / 0.682
5jlj GNPGTP-binding nuclear protein Ran / 0.682
1vg8 GNPRas-related protein Rab-7a / 0.681
2vp0 TTPDeoxynucleoside kinase / 0.681
4cf7 ADPAdenylate kinase / 0.681
1mma ADPMyosin-2 heavy chain / 0.680
3e5h GNPRas-related protein Rab-28 / 0.680
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.679
4z54 GDPNeuronal-specific septin-3 / 0.679
1s1c GNPTransforming protein RhoA / 0.678
3ea5 GDPGTP-binding nuclear protein Ran / 0.678
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.678
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.677
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
1sdm ADPKinesin heavy chain-like protein / 0.677
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
4dxa GSPRas-related protein Rap-1b / 0.677
4hdq GNPRas-related protein Rap-1b / 0.677
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.676
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
3tqc ADPPantothenate kinase / 0.676
3zia ATPATP synthase subunit alpha, mitochondrial / 0.676
1g17 GNPRas-related protein SEC4 / 0.675
1k5d GNPGTP-binding nuclear protein Ran / 0.675
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.675
3oes GNPGTPase RhebL1 / 0.675
3q5d GDPAtlastin-1 3.6.5 0.675
4dls GNPGTPase HRas / 0.675
5c46 GSPRas-related protein Rab-11A / 0.675
5dha GNPGTP-binding nuclear protein Ran / 0.675
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.674
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.674
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.673
4l8g GDPGTPase KRas / 0.673
4lhv GDPRas-related protein Rab-8A / 0.673
4lrw GDPGTPase KRas / 0.673
4qbg AP5Adenylate kinase / 0.672
2c9o ADPRuvB-like 1 3.6.4.12 0.671
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.671
2rgb GNPGTPase HRas / 0.671
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.671
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.670
3ftq GNPSeptin-2 / 0.670
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.670
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.670
4ldj GDPGTPase KRas / 0.670
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.669
1wbb ADPDNA mismatch repair protein MutS / 0.669
1yrs ADPKinesin-like protein KIF11 / 0.669
4nyj GNPGTPase HRas / 0.669
4q02 GDPGTPase KRas / 0.669
1ky2 GNPGTP-binding protein YPT7 / 0.668
1yu9 GNPRas-related protein Rab-4A / 0.668
3kkq GDPRas-related protein M-Ras / 0.668
3rab GNPRas-related protein Rab-3A / 0.668
4ap0 ADPKinesin-like protein KIF11 / 0.668
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.668
4d0l GSPRas-related protein Rab-11A / 0.668
4wa7 GDPGTPase KRas / 0.668
1sq5 ADPPantothenate kinase 2.7.1.33 0.667
1zio AP5Adenylate kinase / 0.667
2bbw GP5Adenylate kinase 4, mitochondrial / 0.667
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.667
3a58 GNPGTP-binding protein RHO1 / 0.667
3k9l GNPGTPase HRas / 0.667
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.667
4epw GDPGTPase KRas / 0.666
4goj GNPADP-ribosylation factor-like protein 3 / 0.666
4pjj ADPUnconventional myosin-VI / 0.666
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.666
1zm7 TTPDeoxynucleoside kinase / 0.665
2rgg GNPGTPase HRas / 0.665
3k1j ADPATP-dependent protease Lon / 0.664
4nyi GNPGTPase HRas / 0.664
4xsg GSPTransforming protein RhoA / 0.664
1uad GNPRas-related protein Ral-A / 0.663
4a28 ADPKinesin-like protein KIF11 / 0.663
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.663
4idp GNPAtlastin-1 3.6.5 0.663
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.662
3qbt GNPRas-related protein Rab-8A / 0.662
4hse ADPChaperone protein ClpB / 0.661
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.660
3d8b ADPFidgetin-like protein 1 3.6.4 0.660
5cyo GDPSeptin-9 / 0.659
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.658
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.658
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.658
4tq9 GDPGTPase KRas / 0.658
1b7t ADPMyosin heavy chain, striated muscle / 0.657
2ql6 ADPNicotinamide riboside kinase 1 / 0.657
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.657
4a1z ADPKinesin-like protein KIF11 / 0.657
4obe GDPGTPase KRas / 0.657
4qbh AP5Adenylate kinase / 0.657
5ftc ADPTPR domain protein / 0.657
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.656
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.656
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.656
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.656
1ny5 ADPTranscriptional regulator (NtrC family) / 0.655
1oix GDPRas-related protein Rab-11A / 0.654
1z0a GDPRas-related protein Rab-2A / 0.654
2v1x ADPATP-dependent DNA helicase Q1 3.6.4.12 0.654
3tlx ADPAdenylate kinase 2 / 0.654
3x1w GDPRas-related protein Rap-1b / 0.654
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.653
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
1rj9 GCPSignal recognition particle receptor FtsY / 0.652
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.652
2pg2 ADPKinesin-like protein KIF11 / 0.652
4jvj 1MVFarnesyl pyrophosphate synthase 2.5.1.10 0.652
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.651
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.651
2hld ANPATP synthase subunit alpha, mitochondrial / 0.651
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2j7p GNPSignal recognition particle protein / 0.651
2j7p GNPSignal recognition particle receptor FtsY / 0.651
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.651
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.651
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.650
2q3f GNPRas-related GTP-binding protein D / 0.650
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.650