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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
1xd9 ADP Nitrogenase iron protein 1 1.18.6.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.877
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.744
2xf3 J01Uncharacterized protein / 0.744
2xvv 9DNSerum albumin / 0.744
3cz0 9ODPheromone-binding protein ASP1 / 0.744
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.744
3nfa CBJGag-Pol polyprotein / 0.744
3nks ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4ivo ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4kla CHDFerrochelatase, mitochondrial 4.99.1.1 0.744
5dby DIFSerum albumin / 0.744
5jqb IBPEnvelope glycoprotein / 0.744
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.707
1wbb ADPDNA mismatch repair protein MutS / 0.706
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.703
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.702
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.702
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.701
4ihq ADPConserved Archaeal protein / 0.697
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.692
3tqc ADPPantothenate kinase / 0.691
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.690
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.690
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.689
3l9h ADPKinesin-like protein KIF11 / 0.689
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.688
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.688
4jl5 ADPAdenylate kinase / 0.688
1s3g AP5Adenylate kinase / 0.687
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.687
3ea0 ATPATPase, ParA family / 0.685
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.684
4gp6 ADPMetallophosphoesterase / 0.681
2zts ADPUncharacterized protein / 0.680
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.680
1w5t ADPORC1-type DNA replication protein 2 / 0.679
2fl2 ADPKinesin-like protein KIF11 / 0.679
4b7b ADPKinesin-like protein KIF11 / 0.679
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.679
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.678
4cf7 ADPAdenylate kinase / 0.678
1ake AP5Adenylate kinase / 0.677
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.677
2qen ADPWalker-Type ATPase / 0.677
3ieu GDPGTPase Era / 0.677
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.677
4ike ADPAdenylate kinase / 0.677
4jky ADPAdenylate kinase / 0.677
4jld ADPAdenylate kinase / 0.677
5ftc ADPTPR domain protein / 0.677
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.676
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2ql6 ADPNicotinamide riboside kinase 1 / 0.676
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.676
2x7e ADPKinesin-like protein KIF11 / 0.675
3ez6 ADPPlasmid partition protein A / 0.674
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.674
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
3k3b ADPKinesin-like protein KIF11 / 0.673
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.672
4nh0 ATPESX secretion system protein EccC / 0.672
4jsy GTPMetallophosphoesterase / 0.671
2zfi ADPKinesin-like protein KIF1A / 0.670
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.670
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.669
4lhv GDPRas-related protein Rab-8A / 0.669
4v02 ATPSite-determining protein / 0.669
4yqf GDPSeptin-9 / 0.669
1ny5 ADPTranscriptional regulator (NtrC family) / 0.668
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.667
2o8b ADPDNA mismatch repair protein Msh2 / 0.667
2zet GTPRas-related protein Rab-27B / 0.667
3c41 ANPAmino acid ABC transporter / 0.667
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.666
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
2zr9 DTPProtein RecA / 0.666
3zia ATPATP synthase subunit alpha, mitochondrial / 0.666
1z0a GDPRas-related protein Rab-2A / 0.665
2xae ADPKinesin-like protein KIF11 / 0.665
4q03 GDPGTPase KRas / 0.665
1w5t ANPORC1-type DNA replication protein 2 / 0.664
2y65 ADPKinesin heavy chain / 0.664
2rgx AP5Adenylate kinase / 0.663
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.663
1sxj ADPReplication factor C subunit 5 / 0.662
2fna ADPUncharacterized protein / 0.662
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.662
2hld ANPATP synthase subunit alpha, mitochondrial / 0.661
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
2iut AGSDNA translocase FtsK / 0.661
2g1q ADPKinesin-like protein KIF11 / 0.660
1xmv ADPProtein RecA / 0.659
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.658
1yrs ADPKinesin-like protein KIF11 / 0.658
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.658
4luc GDPGTPase KRas / 0.658
1jx2 ADPMyosin-2 heavy chain / 0.657
1y3a GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.657
2gil GTPRas-related protein Rab-6A / 0.657
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.657
1l8q ADPChromosomal replication initiator protein DnaA / 0.656
3kb1 ADPIron-sulfur cluster carrier protein / 0.656
4mkf AP5Adenylate kinase / 0.656
4oi2 ADPProtein clpf-1 / 0.656
1sdm ADPKinesin heavy chain-like protein / 0.655
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.655
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.655
3pcr GTPADP-ribosylation factor 6 / 0.654
3qbv GDPCell division control protein 42 homolog / 0.654
4a51 ADPKinesin-like protein KIF11 / 0.654
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.654
1z2c GNPRho-related GTP-binding protein RhoC / 0.653
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
4pjk ADPMyosin-2 heavy chain / 0.653
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.652
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
3cob ADPKinesin heavy chain-like protein / 0.652
3d8b ADPFidgetin-like protein 1 3.6.4 0.652
3k1j ADPATP-dependent protease Lon / 0.652
1ow3 GDPTransforming protein RhoA / 0.651
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.651
4cym GCPRas-related protein Rab-32 / 0.651
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
1mma ADPMyosin-2 heavy chain / 0.650
2gcp GSPRho-related GTP-binding protein RhoC / 0.650
3ftq GNPSeptin-2 / 0.650
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.650
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.650
4hdq GNPRas-related protein Rap-1b / 0.650
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.650