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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
4pl0 ANP Microcin-J25 export ATP-binding/permease protein McjD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 1.137
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.739
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.738
1svm ATPLarge T antigen 3.6.4 0.714
4jsy GTPMetallophosphoesterase / 0.714
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.710
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.707
3c41 ANPAmino acid ABC transporter / 0.705
4qm6 GTPMetallophosphoesterase / 0.705
4dlz GNPGTPase HRas / 0.703
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.701
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.699
4xsg GSPTransforming protein RhoA / 0.699
1kmq GNPTransforming protein RhoA / 0.696
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.696
3l8y GNPGTPase HRas / 0.696
4rkf GNPRas-related protein Rab-3 / 0.695
1ky2 GNPGTP-binding protein YPT7 / 0.694
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.693
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
2oap ANPType II secretion system protein (GspE-2) / 0.692
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.692
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.692
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.692
3rs0 GNPGTPase HRas / 0.691
3rs4 GNPGTPase HRas / 0.691
3rs7 GNPGTPase HRas / 0.691
1nsf ATPVesicle-fusing ATPase 3.6.4.6 0.690
1v8k ANPKinesin-like protein KIF2C / 0.690
5b2z GNPGTPase HRas / 0.690
3rs5 GNPGTPase HRas / 0.689
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.688
4dlt GNPGTPase HRas / 0.688
2rgc GNPGTPase HRas / 0.687
5jlj GNPGTP-binding nuclear protein Ran / 0.687
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.686
4l9w GNPGTPase HRas / 0.686
1q12 ATPMaltose/maltodextrin import ATP-binding protein MalK / 0.684
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.684
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.682
1am4 GNPCell division control protein 42 homolog / 0.681
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.681
4qbg AP5Adenylate kinase / 0.681
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.680
1zbd GTPRas-related protein Rab-3A / 0.679
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.679
3law GNPRas-related protein Rab-7a / 0.679
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.678
3i3s GNPGTPase HRas / 0.678
3k8y GNPGTPase HRas / 0.678
3oiw GNPGTPase HRas / 0.678
3v4f GNPGTPase HRas / 0.678
2rgg GNPGTPase HRas / 0.677
3tso GNPRas-related protein Rab-25 / 0.677
4dlw GNPGTPase HRas / 0.677
4xoi GTPTransforming protein RhoA / 0.677
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
1sxj AGSReplication factor C subunit 1 / 0.674
3wyf GTPGTP-binding nuclear protein / 0.674
2cl6 CAGGTPase HRas / 0.673
3rsl GNPGTPase HRas / 0.673
2cls GTPRho-related GTP-binding protein Rho6 / 0.672
3lbn GNPGTPase HRas / 0.672
4dlx GNPGTPase HRas / 0.672
5dif GNPGTP-binding nuclear protein Ran / 0.672
2fg5 GNPRas-related protein Rab-31 / 0.671
3kz1 GSPTransforming protein RhoA / 0.671
2uyi ADPKinesin-like protein KIF11 / 0.670
4mkg AP5Adenylate kinase / 0.669
1z2c GNPRho-related GTP-binding protein RhoC / 0.667
3oee ANPATP synthase subunit alpha, mitochondrial / 0.667
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
3bxz ADPProtein translocase subunit SecA / 0.666
4c30 ANPDNA helicase / 0.666
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.666
2rgx AP5Adenylate kinase / 0.664
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
3dkv AP5Adenylate kinase / 0.662
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.660
1l2t ATPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.660
1wa5 GTPGTP-binding nuclear protein Ran / 0.659
3m0e ATPTranscriptional regulator (NtrC family) / 0.658
2zr9 DTPProtein RecA / 0.657
3l9h ADPKinesin-like protein KIF11 / 0.657
3lbi GNPGTPase HRas / 0.656
1svl ADPLarge T antigen 3.6.4 0.654
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.654
3adp NAILambda-crystallin 1.1.1.45 0.654
3hqd ANPKinesin-like protein KIF11 / 0.652
1s3s ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.651
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.651
3q2k NAIProbable oxidoreductase / 0.651
4idp GNPAtlastin-1 3.6.5 0.651
4uj5 GNPRas-related protein Rab-11A / 0.651
5dha GNPGTP-binding nuclear protein Ran / 0.651
1s1c GNPTransforming protein RhoA / 0.650
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.650
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.650