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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
2pc9 ATP Phosphoenolpyruvate carboxykinase (ATP)

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.984
2bku GTPGTP-binding nuclear protein Ran / 0.754
1zbd GTPRas-related protein Rab-3A / 0.752
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.747
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.741
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.733
4o25 GTPGTP-binding protein Rheb / 0.731
4jsy GTPMetallophosphoesterase / 0.727
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.726
4qm6 GTPMetallophosphoesterase / 0.725
3m0e ATPTranscriptional regulator (NtrC family) / 0.724
1t91 GTPRas-related protein Rab-7a / 0.723
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.722
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.721
1wdt GTPElongation factor G (EF-G-2) / 0.719
4k81 GTPGTPase HRas / 0.719
4kvg GTPRas-related protein Rap-1A / 0.716
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.714
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.714
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.713
1mmg AGSMyosin-2 heavy chain / 0.711
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.711
4qxa GTPRas-related protein Rab-9A / 0.711
4xoi GTPTransforming protein RhoA / 0.711
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.710
1m7b GTPRho-related GTP-binding protein RhoE / 0.709
4a51 ADPKinesin-like protein KIF11 / 0.709
4qnr ATPPsp operon transcriptional activator / 0.709
3tkl GTPRas-related protein Rab-1A / 0.708
2gil GTPRas-related protein Rab-6A / 0.707
4o2l GTPGTP-binding protein Rheb / 0.706
4xsg GSPTransforming protein RhoA / 0.705
4js0 GNPCell division control protein 42 homolog / 0.704
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.703
1gwn GTPRho-related GTP-binding protein RhoE / 0.703
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.703
4b7b ADPKinesin-like protein KIF11 / 0.703
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.703
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.701
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.701
5c46 GSPRas-related protein Rab-11A / 0.701
2fl2 ADPKinesin-like protein KIF11 / 0.700
2gcp GSPRho-related GTP-binding protein RhoC / 0.700
4mkf AP5Adenylate kinase / 0.700
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.699
2cls GTPRho-related GTP-binding protein Rho6 / 0.699
2zet GTPRas-related protein Rab-27B / 0.699
1yrs ADPKinesin-like protein KIF11 / 0.698
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.698
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.697
2c5l GTPGTPase HRas / 0.697
4dvg GSPRho family GTPase / 0.697
2rgx AP5Adenylate kinase / 0.695
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.695
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.695
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.693
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
1wbb ADPDNA mismatch repair protein MutS / 0.693
3mjh GTPRas-related protein Rab-5A / 0.693
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.693
4lrw GDPGTPase KRas / 0.692
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.691
2xae ADPKinesin-like protein KIF11 / 0.691
2y65 ADPKinesin heavy chain / 0.691
4lpk GDPGTPase KRas / 0.691
4x8o AP5Adenylate kinase / 0.691
1rrg GDPADP-ribosylation factor 1 / 0.690
2pg2 ADPKinesin-like protein KIF11 / 0.690
2zfi ADPKinesin-like protein KIF1A / 0.690
4itr GDPCell division control protein 42 homolog / 0.690
2c96 ATPPsp operon transcriptional activator / 0.689
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.689
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.689
2x2r ADPKinesin-like protein KIF11 / 0.689
3kz1 GSPTransforming protein RhoA / 0.689
4d81 ADPAAA ATPase, central domain protein / 0.689
5ftc ADPTPR domain protein / 0.689
1lfd GNPGTPase HRas / 0.688
1sdm ADPKinesin heavy chain-like protein / 0.688
1xts GTPGTP-binding protein Rheb / 0.687
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.687
2gm1 ADPKinesin-like protein KIF11 / 0.687
2x7e ADPKinesin-like protein KIF11 / 0.687
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.686
3w3z GTPGTP-binding nuclear protein Ran / 0.686
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.686
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.685
1wa5 GTPGTP-binding nuclear protein Ran / 0.685
2eck ADPAdenylate kinase / 0.685
3bbp GTPRas-related protein Rab-6A / 0.685
4qbi AP5Adenylate kinase / 0.685
5fl3 ADPPili retraction protein PilT / 0.685
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.684
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.684
4asu ADPATP synthase subunit alpha, mitochondrial / 0.684
4jl5 ADPAdenylate kinase / 0.684
4qos ADPPsp operon transcriptional activator / 0.684
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.684
4yqf GDPSeptin-9 / 0.684
1g17 GNPRas-related protein SEC4 / 0.683
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.683
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.683
1w5s ADPORC1-type DNA replication protein 2 / 0.682
2ffq GSPRas-related protein Rab-6B / 0.682
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.682
3l9h ADPKinesin-like protein KIF11 / 0.682
1cxz GSPTransforming protein RhoA / 0.681
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.681
2vf7 ADPUvrABC system protein A / 0.681
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.680
2ce2 GDPGTPase HRas / 0.680
3ftq GNPSeptin-2 / 0.679
4d0l GSPRas-related protein Rab-11A / 0.679
4dxa GSPRas-related protein Rap-1b / 0.679
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.678
4hi0 GDPUrease accessory protein UreG / 0.678
5di3 GNPADP-ribosylation factor-like protein 3 / 0.678
2cl6 CAGGTPase HRas / 0.677
3wyf GTPGTP-binding nuclear protein / 0.677
4l8g GDPGTPase KRas / 0.677
3rab GNPRas-related protein Rab-3A / 0.676
4ncl GDPEukaryotic translation initiation factor 5B / 0.676
2c9c ATPPsp operon transcriptional activator / 0.675
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.675
4l9s GDPGTPase HRas / 0.675
4mit GTPRho-related protein racC / 0.675
4obe GDPGTPase KRas / 0.675
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.675
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.674
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.674
4xvu ATPATPase GET3 / 0.674
1a2b GSPTransforming protein RhoA / 0.673
2fg5 GNPRas-related protein Rab-31 / 0.673
3dl0 AP5Adenylate kinase / 0.673
3kkq GDPRas-related protein M-Ras / 0.673
4epw GDPGTPase KRas / 0.673
4o2r GDPGTP-binding protein Rheb / 0.673
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.672
5hpy GDPTransforming protein RhoA / 0.672
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.671
3thy ADPDNA mismatch repair protein Msh2 / 0.671
4epx GDPGTPase KRas / 0.671
4q02 GDPGTPase KRas / 0.671
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.671
2q2z ADPKinesin-like protein KIF11 / 0.670
2ql6 ADPNicotinamide riboside kinase 1 / 0.670
3cph GDPRas-related protein SEC4 / 0.670
3q5d GDPAtlastin-1 3.6.5 0.670
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.670
4gp6 ADPMetallophosphoesterase / 0.670
4lv6 GDPGTPase KRas / 0.670
1d5c GDPGTPase (Rab6) / 0.669
2dpx GDPGTP-binding protein RAD / 0.669
2j5x GSPADP-ribosylation factor 6 / 0.669
1g16 GDPRas-related protein SEC4 / 0.668
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.668
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
2o8b ADPDNA mismatch repair protein Msh2 / 0.667
2r9v ATPATP synthase subunit alpha / 0.667
2zrj AGSProtein RecA / 0.667
3cob ADPKinesin heavy chain-like protein / 0.667
3lbi GNPGTPase HRas / 0.667
4oi2 ADPProtein clpf-1 / 0.667
2fe4 GDPRas-related protein Rab-6B / 0.666
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.666
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.665
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.665
4dsu GDPGTPase KRas / 0.665
4tyq AP5Adenylate kinase / 0.665
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.664
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.664
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.663
3k3b ADPKinesin-like protein KIF11 / 0.663
3kud GDPGTPase HRas / 0.663
3qbv GDPCell division control protein 42 homolog / 0.663
4pfp ADPUnconventional myosin-VI / 0.663
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.662
1z0d GDPRas-related protein Rab-5C / 0.662
1z2a GDPRas-related protein Rab-23 / 0.662
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
3pcr GTPADP-ribosylation factor 6 / 0.662
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.662
4nh0 ATPESX secretion system protein EccC / 0.662
4y0v GDPADP-ribosylation factor 1, putative / 0.662
4ylg GDPADP-ribosylation factor 1, putative / 0.662
1xmv ADPProtein RecA / 0.661
2iut AGSDNA translocase FtsK / 0.661
3ref GDPRho family GTPase / 0.661
3t1t GDPProbable gliding protein mglA / 0.661
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.661
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.660
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.660
3l1c ADPProtein claret segregational / 0.660
2l0x GDPGTP-binding protein Rheb / 0.658
3dkv AP5Adenylate kinase / 0.658
3ea5 GDPGTP-binding nuclear protein Ran / 0.658
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.657
1s1c GNPTransforming protein RhoA / 0.657
3nbz GTPGTP-binding nuclear protein Ran / 0.657
4lhv GDPRas-related protein Rab-8A / 0.657
1yra GDPGPN-loop GTPase PAB0955 / 0.656
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.656
3kuc GDPRas-related protein Rap-1A / 0.656
3lbn GNPGTPase HRas / 0.656
5aun ADPIron-sulfur cluster carrier protein / 0.656
5d3q GDPDynamin-1 3.6.5.5 0.656
1ii6 ADPKinesin-like protein KIF11 / 0.655
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.654
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.653
4mkh AP5Adenylate kinase / 0.653
4tq9 GDPGTPase KRas / 0.653
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.652
3a6p GTPGTP-binding nuclear protein Ran / 0.652
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.652
1tu3 GNPRas-related protein Rab-5A / 0.651
2oo7 AP5Adenylate kinase / 0.651
2qen ADPWalker-Type ATPase / 0.651
3d8b ADPFidgetin-like protein 1 3.6.4 0.650