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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
3zcb ATP Adenosine monophosphate-protein transferase VbhT 2.7.7.n1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.991
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.804
3zec ANPAdenosine monophosphate-protein transferase SoFic 2.7.7.n1 0.790
4u0s ADPAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.753
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.744
4x2d ATPFic family protein putative filamentation induced by cAMP protein / 0.739
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.710
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.702
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.701
4u07 ATPAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.699
3k8t DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.698
2cvv ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.696
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.690
3zcn ATPAdenosine monophosphate-protein transferase SoFic 2.7.7.n1 0.688
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.686
3oab DSTGeranyl diphosphate synthase large subunit / 0.685
2a41 ATPActin, alpha skeletal muscle / 0.684
3ar4 ATPSarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.684
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.684
4xjc TTPdCTP deaminase / 0.684
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.683
2o1o RISPutative farnesyl pyrophosphate synthase / 0.683
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.679
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.678
3krf DSTGeranyl diphosphate synthase large subunit / 0.678
3a5m ATPMajor actin / 0.675
1t91 GTPRas-related protein Rab-7a / 0.674
2r4t ADPGlycogen synthase 2.4.1.21 0.674
2r4u ADPGlycogen synthase 2.4.1.21 0.674
2x60 GTPMannose-1-phosphate guanylyltransferase / 0.674
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.674
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.672
3mn7 ATPActin-5C / 0.672
3w3d ATPActin, gamma-enteric smooth muscle / 0.672
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.671
3tsc NADUncharacterized protein / 0.671
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.669
3a5o ATPMajor actin / 0.668
3c1o NAPEugenol synthase / 0.668
3mvw BHZNickel-binding periplasmic protein / 0.668
4pl8 ATPActin, alpha skeletal muscle / 0.668
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.667
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.666
3orl AGSSerine/threonine protein kinase / 0.665
4dwb 0M7Farnesyl pyrophosphate synthase / 0.665
4kvg GTPRas-related protein Rap-1A / 0.665
1svm ATPLarge T antigen 3.6.4 0.664
4a6a TTPdCTP deaminase 3.5.4.13 0.663
2wgh DTPRibonucleoside-diphosphate reductase large subunit 1.17.4.1 0.661
4dxj 0M9Farnesyl pyrophosphate synthase / 0.661
5i4n ATPTyrosine-protein kinase JAK2 / 0.661
1wa5 GTPGTP-binding nuclear protein Ran / 0.660
2oap ANPType II secretion system protein (GspE-2) / 0.660
2ofi ADK3-methyladenine DNA glycosylase I / 0.660
4fvq ATPTyrosine-protein kinase JAK2 / 0.660
4xoi GTPTransforming protein RhoA / 0.660
1wua ATPActin, alpha skeletal muscle / 0.659
4fvr ATPTyrosine-protein kinase JAK2 / 0.659
4qm6 GTPMetallophosphoesterase / 0.658
2q36 ATPActin, alpha skeletal muscle / 0.656
3dyh 721Farnesyl pyrophosphate synthase / 0.656
3ruv ANPChaperonin / 0.656
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.655
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.655
3mn9 ATPActin-5C / 0.655
3s55 NADPutative short-chain dehydrogenase/reductase / 0.655
1foa UD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase 2.4.1.101 0.654
1i7c MGBS-adenosylmethionine decarboxylase proenzyme 4.1.1.50 0.654
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.654
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.653
2bp1 NDPAflatoxin B1 aldehyde reductase member 2 / 0.653
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.653
4geb 0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial 2.6.1.39 0.653
4nke RISFarnesyl pyrophosphate synthase 2.5.1.10 0.653
1ky2 GNPGTP-binding protein YPT7 / 0.652
1n2e APCPantothenate synthetase 6.3.2.1 0.652
2bku GTPGTP-binding nuclear protein Ran / 0.652
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
3ffk ATPActin, alpha skeletal muscle / 0.652
2c5l GTPGTPase HRas / 0.651
3daw ATPActin, alpha skeletal muscle / 0.651
3o0q TTPVitamin B12-dependent ribonucleotide reductase / 0.651
3w3z GTPGTP-binding nuclear protein Ran / 0.651
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.651
3cgc COACoenzyme A disulfide reductase / 0.650
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.650