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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
2jlr ANP Genome polyprotein 3.4.21.91

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2jlr ANPGenome polyprotein 3.4.21.91 1.048
2bc9 GNPGuanylate-binding protein 1 / 0.825
1kmq GNPTransforming protein RhoA / 0.823
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.822
2c5l GTPGTPase HRas / 0.820
1xtr GNPGTP-binding protein Rheb / 0.819
1s1c GNPTransforming protein RhoA / 0.818
4idn GNPAtlastin-1 3.6.5 0.818
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.817
3rs7 GNPGTPase HRas / 0.817
3lbn GNPGTPase HRas / 0.816
4dlw GNPGTPase HRas / 0.816
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.815
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.814
3w3z GTPGTP-binding nuclear protein Ran / 0.813
1z2c GNPRho-related GTP-binding protein RhoC / 0.812
3ftq GNPSeptin-2 / 0.811
5dha GNPGTP-binding nuclear protein Ran / 0.811
3b1x GNPFerrous iron transport protein B / 0.809
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.807
2rgg GNPGTPase HRas / 0.802
3i3s GNPGTPase HRas / 0.802
3k9l GNPGTPase HRas / 0.802
3lbi GNPGTPase HRas / 0.802
3oes GNPGTPase RhebL1 / 0.802
3pit GNPRas-related protein M-Ras / 0.802
3tgp GNPGTPase HRas / 0.802
3x1z GNPRas-related protein Rap-1b / 0.802
3k8y GNPGTPase HRas / 0.801
3oiv GNPGTPase HRas / 0.800
3oiw GNPGTPase HRas / 0.800
4dls GNPGTPase HRas / 0.800
1ky2 GNPGTP-binding protein YPT7 / 0.799
3qbt GNPRas-related protein Rab-8A / 0.799
4rkf GNPRas-related protein Rab-3 / 0.796
3rab GNPRas-related protein Rab-3A / 0.793
1okk GCPSignal recognition particle protein / 0.791
1okk GCPSignal recognition particle receptor FtsY / 0.791
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.791
1wa5 GTPGTP-binding nuclear protein Ran / 0.790
1wdt GTPElongation factor G (EF-G-2) / 0.789
2j7p GNPSignal recognition particle protein / 0.789
2j7p GNPSignal recognition particle receptor FtsY / 0.789
1uad GNPRas-related protein Ral-A / 0.787
2rgb GNPGTPase HRas / 0.787
3ddc GNPGTPase HRas / 0.787
4l9w GNPGTPase HRas / 0.787
2rge GNPGTPase HRas / 0.786
3oiu GNPGTPase HRas / 0.786
3rs0 GNPGTPase HRas / 0.786
3rs4 GNPGTPase HRas / 0.786
3rs5 GNPGTPase HRas / 0.786
3rsl GNPGTPase HRas / 0.786
4dlt GNPGTPase HRas / 0.786
4dlv GNPGTPase HRas / 0.786
4hdq GNPRas-related protein Rap-1b / 0.786
4xsg GSPTransforming protein RhoA / 0.786
2rgc GNPGTPase HRas / 0.785
3l8y GNPGTPase HRas / 0.785
3lbh GNPGTPase HRas / 0.785
3v4f GNPGTPase HRas / 0.785
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.785
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.784
3kko GNPRas-related protein M-Ras / 0.784
4dlx GNPGTPase HRas / 0.784
4dlz GNPGTPase HRas / 0.784
4nyj GNPGTPase HRas / 0.784
4xvq GNPGTPase HRas / 0.784
5b2z GNPGTPase HRas / 0.784
5dif GNPGTP-binding nuclear protein Ran / 0.783
5l3s GNPSignal recognition particle receptor FtsY / 0.783
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.780
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.780
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.780
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.779
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.779
1esn ANPPantothenate kinase 2.7.1.33 0.778
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.777
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.776
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.775
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.774
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.773
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.770
5di3 GNPADP-ribosylation factor-like protein 3 / 0.770
4c2u ANPDNA helicase / 0.769
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.768
3zfd ANPChromosome-associated kinesin KIF4 / 0.768
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.768
4xoi GTPTransforming protein RhoA / 0.768
1lfd GNPGTPase HRas / 0.766
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.766
4idp GNPAtlastin-1 3.6.5 0.766
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.765
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.765
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.765
1gwn GTPRho-related GTP-binding protein RhoE / 0.763
1t91 GTPRas-related protein Rab-7a / 0.763
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.762
3myk ANPMyosin-2 heavy chain / 0.762
1fmw ATPMyosin-2 heavy chain / 0.761
3kz1 GSPTransforming protein RhoA / 0.761
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.760
1ibr GNPGTP-binding nuclear protein Ran / 0.759
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.759
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.758
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.757
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.757
3c41 ANPAmino acid ABC transporter / 0.757
1mmg AGSMyosin-2 heavy chain / 0.756
1w5t ANPORC1-type DNA replication protein 2 / 0.754
1v8k ANPKinesin-like protein KIF2C / 0.752
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.752
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.752
4dso GSPGTPase KRas / 0.748
4ohv ANPProtein clpf-1 / 0.748
3zia ATPATP synthase subunit alpha, mitochondrial / 0.747
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.743
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.741
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.741
4goj GNPADP-ribosylation factor-like protein 3 / 0.739
2y65 ADPKinesin heavy chain / 0.737
4dvg GSPRho family GTPase / 0.737
1xms ANPProtein RecA / 0.736
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.736
3law GNPRas-related protein Rab-7a / 0.735
1cxz GSPTransforming protein RhoA / 0.732
1sdm ADPKinesin heavy chain-like protein / 0.732
4ihq ADPConserved Archaeal protein / 0.732
2x2r ADPKinesin-like protein KIF11 / 0.730
1z0f GDPRas-related protein Rab-14 / 0.729
4luc GDPGTPase KRas / 0.729
4obe GDPGTPase KRas / 0.729
5ftc ADPTPR domain protein / 0.729
2gm1 ADPKinesin-like protein KIF11 / 0.728
2qen ADPWalker-Type ATPase / 0.728
2xae ADPKinesin-like protein KIF11 / 0.728
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.727
4asu ADPATP synthase subunit alpha, mitochondrial / 0.727
4mit GTPRho-related protein racC / 0.727
4v02 ATPSite-determining protein / 0.727
2cls GTPRho-related GTP-binding protein Rho6 / 0.726
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.726
2r9v ATPATP synthase subunit alpha / 0.726
4c30 ANPDNA helicase / 0.726
2whx ADPGenome polyprotein 3.4.21.91 0.725
3cob ADPKinesin heavy chain-like protein / 0.725
1am4 GNPCell division control protein 42 homolog / 0.724
2gcp GSPRho-related GTP-binding protein RhoC / 0.724
4be7 ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.724
2bme GNPRas-related protein Rab-4A / 0.722
2q3f GNPRas-related GTP-binding protein D / 0.722
4dsu GDPGTPase KRas / 0.722
4lrw GDPGTPase KRas / 0.720
4cym GCPRas-related protein Rab-32 / 0.719
5c46 GSPRas-related protein Rab-11A / 0.719
1jx2 ADPMyosin-2 heavy chain / 0.717
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.717
5cyo GDPSeptin-9 / 0.717
4hdo GNPRas-related protein Rap-1b / 0.716
4uj3 GNPRas-related protein Rab-11A / 0.716
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.715
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.714
3tkl GTPRas-related protein Rab-1A / 0.714
3hqd ANPKinesin-like protein KIF11 / 0.711
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.710
4cid ANPEH domain-containing protein 2 / 0.710
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.708
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.708
4js0 GNPCell division control protein 42 homolog / 0.708
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.705
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.704
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.704
1m7b GTPRho-related GTP-binding protein RhoE / 0.704
1rrg GDPADP-ribosylation factor 1 / 0.703
3fkq ATPNtrC-like two-domain protein / 0.702
2rgx AP5Adenylate kinase / 0.700
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.700
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.699
4zca ADPKinesin-like protein KIF11 / 0.698
1fnn ADPORC1-type DNA replication protein / 0.697
4o2l GTPGTP-binding protein Rheb / 0.697
5k5z ANPUncharacterized protein / 0.697
4pfp ADPUnconventional myosin-VI / 0.695
1vg8 GNPRas-related protein Rab-7a / 0.694
1yu9 GNPRas-related protein Rab-4A / 0.694
2a5y ATPCell death protein 4 / 0.694
1nly AGSCag alpha / 0.693
2w02 ATPAcsD / 0.693
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.693
4qnr ATPPsp operon transcriptional activator / 0.693
3oee ANPATP synthase subunit alpha, mitochondrial / 0.692
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.692
4b7b ADPKinesin-like protein KIF11 / 0.692
1yrs ADPKinesin-like protein KIF11 / 0.691
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.690
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.690
3tso GNPRas-related protein Rab-25 / 0.690
4a1z ADPKinesin-like protein KIF11 / 0.690
5irn ADPNucleotide binding oligomerization domain containing 2 / 0.690
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.689
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.689
1svl ADPLarge T antigen 3.6.4 0.689
1zm7 TTPDeoxynucleoside kinase / 0.689
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.689
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.687
2dr3 ADPUPF0273 protein PH0284 / 0.686
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.685
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.685
4yqf GDPSeptin-9 / 0.685
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.684
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.683
2fg5 GNPRas-related protein Rab-31 / 0.683
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.683
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.683
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.681
2x0q ATPAlcaligin biosynthesis protein / 0.681
4lhw GNPRas-related protein Rab-8A / 0.680
3kud GDPGTPase HRas / 0.679
4cf7 ADPAdenylate kinase / 0.679
4o25 GTPGTP-binding protein Rheb / 0.679
1a2b GSPTransforming protein RhoA / 0.678
3vhx GTPADP-ribosylation factor 6 / 0.678
2bku GTPGTP-binding nuclear protein Ran / 0.677
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.677
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.677
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.677
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.676
3r9x GNPGTPase Era / 0.676
4qm6 GTPMetallophosphoesterase / 0.676
3g6x DGTDNA polymerase iota 2.7.7.7 0.674
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.672
1p9w ANPType II secretion system protein E / 0.671
3a58 GNPGTP-binding protein RHO1 / 0.671
4ohx ADPProtein clpf-1 / 0.671
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.671
4db1 ANPMyosin-7 / 0.670
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.669
2x3j ATPAcsD / 0.669
4dtj TTPDNA-directed DNA polymerase / 0.669
4fjl DGTDNA-directed DNA polymerase / 0.669
4tyq AP5Adenylate kinase / 0.669
5fl3 ADPPili retraction protein PilT / 0.669
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.668
3ne6 DCPDNA-directed DNA polymerase / 0.668
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.668
4fjm DCPDNA-directed DNA polymerase / 0.668
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
1sq5 ADPPantothenate kinase 2.7.1.33 0.667
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
3sup DCPDNA-directed DNA polymerase / 0.667
3tqc ADPPantothenate kinase / 0.667
3lzj CTPDNA-directed DNA polymerase / 0.666
4fjj TTPDNA-directed DNA polymerase / 0.666
3kuc GDPRas-related protein Rap-1A / 0.665
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.665
4dtp DGTDNA-directed DNA polymerase / 0.665
4fjh DGTDNA-directed DNA polymerase / 0.665
3d8b ADPFidgetin-like protein 1 3.6.4 0.664
4nyi GNPGTPase HRas / 0.663
2q2y ADPKinesin-like protein KIF11 / 0.662
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.662
4a51 ADPKinesin-like protein KIF11 / 0.662
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.661
4dtx TTPDNA-directed DNA polymerase / 0.661
4d81 ADPAAA ATPase, central domain protein / 0.660
4m3t ATPDNA-directed DNA polymerase / 0.660
5da9 AGSUncharacterized protein / 0.660
1ow3 GDPTransforming protein RhoA / 0.659
3haz FADBifunctional protein PutA / 0.659
3k1j ADPATP-dependent protease Lon / 0.659
4fj5 DTPDNA-directed DNA polymerase / 0.659
4m42 ATPDNA-directed DNA polymerase / 0.659
4epx GDPGTPase KRas / 0.657
4jsy GTPMetallophosphoesterase / 0.657
1w5s ADPORC1-type DNA replication protein 2 / 0.656
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.655
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.655
4l8g GDPGTPase KRas / 0.655
4xvu ATPATPase GET3 / 0.655
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.654
2gyw OBIAcetylcholinesterase 3.1.1.7 0.654
2yeg XQGHeat shock protein HSP 90-alpha / 0.654
3e2s FADBifunctional protein PutA 1.5.5.2 0.654
4rxp DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.654
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.653
4lv6 GDPGTPase KRas / 0.653
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.652
4epw GDPGTPase KRas / 0.651
1mq4 ADPAurora kinase A 2.7.11.1 0.650
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.650
2j5x GSPADP-ribosylation factor 6 / 0.650
3eg5 GNPCell division control protein 42 homolog / 0.650
4ys0 ADPProtein translocase subunit SecA / 0.650