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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3dkvAP5Adenylate kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3dkvAP5Adenylate kinase/1.000
3dl0AP5Adenylate kinase/0.651
4qbiAP5Adenylate kinase/0.634
2oo7AP5Adenylate kinase/0.626
3hpqAP5Adenylate kinase/0.625
2osbAP5Adenylate kinase/0.616
4qbhAP5Adenylate kinase/0.611
1p3jAP5Adenylate kinase/0.590
4nu0AP5Adenylate kinase/0.588
4mkfAP5Adenylate kinase/0.586
4x8oAP5Adenylate kinase/0.586
1ankANPAdenylate kinase/0.579
4jl6ADPAdenylate kinase/0.579
4w5jAP5Adenylate kinase/0.574
4ikeADPAdenylate kinase/0.567
4cf7ADPAdenylate kinase/0.556
4jkyADPAdenylate kinase/0.552
2eckADPAdenylate kinase/0.547
1akeAP5Adenylate kinase/0.545
1zioAP5Adenylate kinase/0.541
4jldADPAdenylate kinase/0.539
2akyAP5Adenylate kinase/0.538
4x8lAP5Adenylate kinase/0.534
4jl5ADPAdenylate kinase/0.531
2rgxAP5Adenylate kinase/0.508
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.482
5jlaNADPutative short-chain dehydrogenase/reductase/0.476
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.472
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.472
3zkyWT4Isopenicillin N synthase1.21.3.10.470
1qjfACSIsopenicillin N synthase1.21.3.10.469
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.469
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.469
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.469
2bunFADAppA protein/0.467
2cduFADNADH oxidase/0.467
1oc1ASVIsopenicillin N synthase1.21.3.10.465
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.465
2yutNAPPutative short-chain oxidoreductase/0.464
3s79ASDAromatase1.14.14.140.464
3tlxADPAdenylate kinase 2/0.463
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.463
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.462
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.462
3rj9NADAlcohol dehydrogenase1.1.1.10.462
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.461
4be7ATPType I restriction enzyme EcoR124II R protein3.1.21.30.460
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
4in44IDKelch-like ECH-associated protein 1/0.460
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.459
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.459
2c29NAPDihydroflavonol 4-reductase/0.458
3mw9NAIGlutamate dehydrogenase 1, mitochondrial1.4.1.30.458
2ylrNAPPhenylacetone monooxygenase1.14.13.920.457
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.456
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.456
1dr2TAPDihydrofolate reductase1.5.1.30.455
3ed1GA3Gibberellin receptor GID1/0.455
3lqfNADGalactitol dehydrogenase/0.455
4l9q9TPSerum albumin/0.454
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.453
4dieC5PCytidylate kinase/0.453
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
2c27ACOMycothiol acetyltransferase2.3.1.1890.452
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.452
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.452
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.452
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.452
1e3eNAIAlcohol dehydrogenase 41.1.1.10.451
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.451
2v9jATP5'-AMP-activated protein kinase subunit gamma-1/0.451
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
3zoiM2WIsopenicillin N synthase1.21.3.10.451
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.451
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.451
1blzACVIsopenicillin N synthase1.21.3.10.450
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.450
1u1cBAUUridine phosphorylase2.4.2.30.450
2vcmM11Isopenicillin N synthase1.21.3.10.450
3qlrNDPDihydrofolate reductase1.5.1.30.450
4enhFVXCholesterol 24-hydroxylase/0.450
4u0oMTALipoyl synthase 2/0.450
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.450
3av7KYAUncharacterized protein/0.449
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.449
3t3r9PLCytochrome P450 2A61.14.130.449
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.448
1pjkANPCasein kinase II subunit alpha2.7.11.10.448
2dteNAIGlucose 1-dehydrogenase related protein/0.448
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.448
3cisATPUniversal stress protein Rv2623/0.448
4dzzADPPlasmid partitioning protein ParF/0.448
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.448
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.448
5kghACOPredicted acetyltransferase/0.448
1necFMNOxygen-insensitive NAD(P)H nitroreductase10.447
1pq944BOxysterols receptor LXR-beta/0.447
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.447
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.447
1snyNAPLD36273p/0.447
1udbUFGUDP-glucose 4-epimerase5.1.3.20.447
1w5tANPORC1-type DNA replication protein 2/0.447
3l77NJPShort-chain alcohol dehydrogenase/0.447
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.447
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.447
4ki8ADP60 kDa chaperonin/0.447
4n9iPCGCatabolite expression activator/0.447
1i7lATPSynapsin-2/0.446
1tqf32PBeta-secretase 13.4.23.460.446
2bu9HFVIsopenicillin N synthase1.21.3.10.446
2i0aMUIProtease/0.446
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
3bac3B9DNA ligase/0.446
3gbuATPUncharacterized sugar kinase PH14592.7.10.446
3s1dZIRCytokinin dehydrogenase 11.5.99.120.446
4dbzNDPPutative ketoacyl reductase1.3.10.446
4dfrMTXDihydrofolate reductase1.5.1.30.446
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.445
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
1pr9NAPL-xylulose reductase1.1.1.100.445
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.445
2x6tNAPADP-L-glycero-D-manno-heptose-6-epimerase/0.445
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.445
4bfzZVZPantothenate kinase2.7.1.330.445
4okx198Androgen receptor/0.445
4x9mFADUncharacterized protein MG039 homolog/0.445
5dozNDPJamJ/0.445
1rfvADPPyridoxal kinase2.7.1.350.444
2bxmIMNSerum albumin/0.444
3uceNDPDehydrogenase/0.444
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.444
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.443
1u3dFADCryptochrome-1/0.443
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.443
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.443
2qrdADP5'-AMP-activated protein kinase subunit gamma/0.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
3mpt1GKMitogen-activated protein kinase 14/0.443
3r9iADPSeptum site-determining protein MinD/0.443
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
4ruoBIVVitamin D3 receptor A/0.443
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.443
1pd9CO4Dihydrofolate reductase1.5.1.30.442
1w4zNAPPutative ketoacyl reductase1.3.10.442
1x7hNDPPutative ketoacyl reductase1.3.10.442
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2e20B4PPropionate kinase/0.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
3drcMTXDihydrofolate reductase1.5.1.30.442
3ijrNADOxidoreductase, short chain dehydrogenase/reductase family/0.442
3nx4NAPPutative oxidoreductase/0.442
3qfrNAPNADPH--cytochrome P450 reductase/0.442
3zeiAWHO-acetylserine sulfhydrylase/0.442
1a72PADAlcohol dehydrogenase E chain1.1.1.10.441
1bygSTUTyrosine-protein kinase CSK/0.441
1cf3FADGlucose oxidase1.1.3.40.441
1hb1OCVIsopenicillin N synthase1.21.3.10.441
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.441
1q3gUDAUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.441
3flwFLWMitogen-activated protein kinase 14/0.441
3i0pNADMalate dehydrogenase, putative/0.441
3qe2NAPNADPH--cytochrome P450 reductase/0.441
3tqcADPPantothenate kinase/0.441
4eo3FMNBacterioferritin comigratory protein/NADH dehydrogenase/0.441
4gk3L87Ephrin type-A receptor 32.7.10.10.441
4kb81QOCasein kinase I isoform delta2.7.11.10.441
4m4922YL-lactate dehydrogenase A chain1.1.1.270.441
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.440
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.440
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.440
2h55DZ8Heat shock protein HSP 90-alpha/0.440
2npaMMBPeroxisome proliferator-activated receptor alpha/0.440
2qo9ANPEphrin type-A receptor 32.7.10.10.440
2vbpVB1Isopenicillin N synthase1.21.3.10.440
2w71L23Biotin carboxylase6.3.4.140.440
3cosNADAlcohol dehydrogenase 41.1.1.10.440
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3rkuNAPNADP-dependent 3-hydroxy acid dehydrogenase/0.440
4bb3KKAIsopenicillin N synthase1.21.3.10.440
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.440
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440