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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
5c6cCMPcGMP-dependent protein kinase 22.7.11.12

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5c6cCMPcGMP-dependent protein kinase 22.7.11.121.000
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.540
1pq944BOxysterols receptor LXR-beta/0.523
1pqc444Oxysterols receptor LXR-beta/0.517
1xddAAYIntegrin alpha-L/0.506
2po7CHDFerrochelatase, mitochondrial4.99.1.10.506
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.499
1oc1ASVIsopenicillin N synthase1.21.3.10.488
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.487
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.485
2jh0701Prothrombin3.4.21.50.485
4n9iPCGCatabolite expression activator/0.485
1fmlRTLRetinol dehydratase/0.483
3ocpCMPcGMP-dependent protein kinase 12.7.11.120.483
1d6w00RProthrombin3.4.21.50.482
5dp2NAPCurF/0.482
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.481
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.481
1nm6L86Prothrombin3.4.21.50.480
1d3dBZTProthrombin3.4.21.50.479
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.479
3vf60H6Glucokinase2.7.1.20.479
4ryvZEAProtein LlR18A/0.479
1d3pBT3Prothrombin3.4.21.50.476
2anmCDOProthrombin3.4.21.50.476
4bb3KKAIsopenicillin N synthase1.21.3.10.476
1upw444Oxysterols receptor LXR-beta/0.475
1yplRA8Prothrombin3.4.21.50.475
4uugPXGBranched-chain amino acid aminotransferase, putative/0.473
1nzq162Prothrombin3.4.21.50.472
2cf9348Prothrombin3.4.21.50.472
1ta6177Prothrombin3.4.21.50.471
2r0cFADPutative FAD-monooxygenase/0.471
3ekuCY9Actin-5C/0.471
3p62FMNPentaerythritol tetranitrate reductase/0.471
2cn0F25Prothrombin3.4.21.50.470
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.470
4iarERM5-hydroxytryptamine receptor 1B/0.470
2r2mI50Prothrombin3.4.21.50.469
3hu1AGSTransitional endoplasmic reticulum ATPase3.6.4.60.469
4bfsZVSPantothenate kinase2.7.1.330.469
1d4pBPPProthrombin3.4.21.50.467
1x1cSAHC-20 methyltransferase/0.467
3biz61EWee1-like protein kinase2.7.10.20.467
1ypeUIPProthrombin3.4.21.50.466
2vbpVB1Isopenicillin N synthase1.21.3.10.466
3lu8IQXSerum albumin/0.466
4bfuZVUPantothenate kinase2.7.1.330.466
4bfxZVXPantothenate kinase2.7.1.330.466
1cf3FADGlucose oxidase1.1.3.40.465
1qjfACSIsopenicillin N synthase1.21.3.10.465
2cf8ESHProthrombin3.4.21.50.465
1c4uIH1Prothrombin3.4.21.50.464
3l77NJPShort-chain alcohol dehydrogenase/0.464
3p74FMNPentaerythritol tetranitrate reductase/0.464
1k22MELProthrombin3.4.21.50.463
2geuCOKPantothenate kinase2.7.1.330.463
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.463
2vkeTACTetracycline repressor protein class D/0.463
2x7hPFNProstaglandin reductase 310.463
3gtsD3MDdmC/0.463
1hb1OCVIsopenicillin N synthase1.21.3.10.462
1qorNDPQuinone oxidoreductase 1/0.462
1x1bSAHC-20 methyltransferase/0.462
2in6839Wee1-like protein kinase2.7.10.20.462
3fhxPXLPyridoxal kinase2.7.1.350.462
4b1rITCTetracycline repressor protein class D/0.462
1hfqMOTDihydrofolate reductase1.5.1.30.461
1vbiNADMalate/L-lactate dehydrogenase family protein/0.461
2y6fM9FIsopenicillin N synthase1.21.3.10.461
3hl0NADMaleylacetate reductase/0.461
2iviACWIsopenicillin N synthase1.21.3.10.460
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.460
2vbdV10Isopenicillin N synthase1.21.3.10.460
2xviFADPutative flavin-containing monooxygenase/0.460
3zkyWT4Isopenicillin N synthase1.21.3.10.460
1ygjRMCPyridoxal kinase2.7.1.350.459
1zgi382Prothrombin3.4.21.50.459
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.459
3eksCY9Actin-5C/0.459
3ghh2NFCD38 molecule/0.459
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.459
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.459
1k6pXN3Gag-Pol polyprotein3.4.23.160.458
1vyrFMNPentaerythritol tetranitrate reductase/0.458
2y60M8FIsopenicillin N synthase1.21.3.10.458
3od0PCGcGMP-dependent protein kinase 12.7.11.120.458
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.458
4bfvZVVPantothenate kinase2.7.1.330.458
1blzACVIsopenicillin N synthase1.21.3.10.457
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.457
4u7wNDPMxaA/0.457
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.457
4xnw2IDP2Y purinoceptor 1/0.457
1x1dSAHC-20 methyltransferase/0.456
2bjsACVIsopenicillin N synthase1.21.3.10.456
2cwfNDPDelta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase/0.456
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.456
2uuk897Prothrombin3.4.21.50.456
3gb4D3MDdmC/0.456
3slkNDPPolyketide synthase extender module 2/0.456
3vx4ATPPutative ABC transporter, ATP-binding protein ComA/0.456
3zkuHCVIsopenicillin N synthase1.21.3.10.456
4cdmFO1Deoxyribodipyrimidine photolyase/0.456
4lxa1YSBeta-secretase 13.4.23.460.456
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.456
3emlZMAAdenosine receptor A2a/0.456
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.455
1k6cMK1Gag-Pol polyprotein3.4.23.160.455
1oytFSNProthrombin3.4.21.50.455
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.455
3c36KAIGlutamate receptor ionotropic, kainate 1/0.455
3cr0809Wee1-like protein kinase2.7.10.20.455
4l8u9AZSerum albumin/0.455
1ypjUIBProthrombin3.4.21.50.454
2p5uNADUDP-glucose 4-epimerase/0.454
2rabNADGlutathione amide reductase/0.454
3h3sH15Collagen type IV alpha-3-binding protein/0.454
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.454
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.454
5jscFADPutative acyl-CoA dehydrogenase/0.454
1hb3SCVIsopenicillin N synthase1.21.3.10.453
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.453
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.453
1mueCDDProthrombin3.4.21.50.453
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.453
3nmpPYVAbscisic acid receptor PYL2/0.453
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.453
3w6hAZMCarbonic anhydrase 14.2.1.10.453
4hjoAQ4Epidermal growth factor receptor2.7.10.10.453
4n3l2FNProthrombin3.4.21.50.453
1r2jFADFkbI/0.452
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.452
2zhw12UProthrombin3.4.21.50.452
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.452
3hy7097A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.452
3n0hTOPDihydrofolate reductase1.5.1.30.452
4ks8B49Serine/threonine-protein kinase PAK 62.7.11.10.452
1p8dCO1Oxysterols receptor LXR-beta/0.451
2g8yNADHydroxycarboxylate dehydrogenase B/0.451
2gesCOKPantothenate kinase2.7.1.330.451
2iyaZIOOleandomycin glycosyltransferase/0.451
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.451
2z2w770Wee1-like protein kinase2.7.10.20.451
3bi6396Wee1-like protein kinase2.7.10.20.451
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3hu2AGSTransitional endoplasmic reticulum ATPase3.6.4.60.451
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.451
3q44D50M1 family aminopeptidase3.4.110.451
4g47TZFMycocyclosin synthase1.14.21.90.451
4jx1CAHCamphor 5-monooxygenase1.14.15.10.451
1fmjRTLRetinol dehydratase/0.450
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.450
2vwqNAPGlucose 1-dehydrogenase/0.450
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.450
3jzdNADMaleylacetate reductase/0.450
4ambDUDPutative glycosyl transferase/0.450
4dk70KSOxysterols receptor LXR-beta/0.450
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.450
1i6xCMPcAMP-activated global transcriptional regulator CRP/0.449
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.449
2cftPLPPyridoxal phosphate phosphatase/0.449
2jh6894Prothrombin3.4.21.50.449
2w6qOA5Biotin carboxylase6.3.4.140.449
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3udq09EBeta-secretase 13.4.23.460.449
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
4kb9G79Protease/0.449
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.448
1nzdUPGDNA beta-glucosyltransferase/0.448
1svlADPLarge T antigen3.6.40.448
1yhjR6CPyridoxal kinase2.7.1.350.448
2gvcFADThiol-specific monooxygenase1.14.130.448
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.448
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3tdaPN0Cytochrome P450 2D6/0.448
4ayy9MXProthrombin3.4.21.50.448
4bamMM9Prothrombin3.4.21.50.448
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.448
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.448
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.448
4zzjCNANAD-dependent protein deacetylase sirtuin-13.5.10.448
3uzcT4EAdenosine receptor A2a/0.448
1jwtBLIProthrombin3.4.21.50.447
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.447
1xm1GAHProthrombin3.4.21.50.447
2dq7STUTyrosine-protein kinase Fyn2.7.10.20.447
2io6330Wee1-like protein kinase2.7.10.20.447
2jb4A14Isopenicillin N synthase1.21.3.10.447
2ym1FADPhenylacetone monooxygenase1.14.13.920.447
3arvSAUChitinase A/0.447
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.447
4c4oNADSADH/0.447
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.447
1cjkFOKAdenylate cyclase type 2/0.446
1cjkFOKAdenylate cyclase type 5/0.446
1qiqACCIsopenicillin N synthase1.21.3.10.446
1t4u81AProthrombin3.4.21.50.446
3e8xNAPBH1520 protein/0.446
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.446
3ig6438Urokinase-type plasminogen activator3.4.21.730.446
3jynNDPQuinone oxidoreductase/0.446
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.446
1ae8AZLProthrombin3.4.21.50.445
1crbRTLRetinol-binding protein 1/0.445
1obnASVIsopenicillin N synthase1.21.3.10.445
1z71L17Prothrombin3.4.21.50.445
2cduFADNADH oxidase/0.445
2nr4FMNConserved protein/0.445
2qs1UB1Glutamate receptor ionotropic, kainate 1/0.445
2zfq45UProthrombin3.4.21.50.445
2zhe13UProthrombin3.4.21.50.445
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.445
3af0GDPPantothenate kinase2.7.1.330.445
3fhxPLPPyridoxal kinase2.7.1.350.445
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3jv7NADSecondary alcohol dehydrogenase/0.445
4jqh1MFAlr2278 protein/0.445
4klnAGSTransitional endoplasmic reticulum ATPase3.6.4.60.445
1kmvLIIDihydrofolate reductase1.5.1.30.444
2gjlFMNNitronate monooxygenase1.13.12.160.444
2jh5895Prothrombin3.4.21.50.444
2ph5NADHomospermidine synthase/0.444
2puiADPMethylthioribose kinase2.7.1.1000.444
3b03VNRIsopentenyl-diphosphate delta-isomerase/0.444
3bgcLJHGag-Pol polyprotein3.4.23.160.444
3cqeP91Wee1-like protein kinase2.7.10.20.444
3hk1B64Fatty acid-binding protein, adipocyte/0.444
3i59N6SCRP-like cAMP-activated global transcriptional regulator/0.444
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
4bfwZVWPantothenate kinase2.7.1.330.444
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.444
5irnADPNucleotide binding oligomerization domain containing 2/0.444
1bmfANPATP synthase subunit alpha, mitochondrial/0.443
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.443
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
1h51FMNPentaerythritol tetranitrate reductase/0.443
1v35NAIEnoyl-ACP reductase/0.443
1vikBAYGag-Pol polyprotein/0.443
2b8jADNClass B acid phosphatase3.1.3.20.443
2vn0TDZCytochrome P450 2C8/0.443
2ym2NAPPhenylacetone monooxygenase1.14.13.920.443
2zc922UProthrombin3.4.21.50.443
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.443
3uyk0CXProbable NDP-rhamnosyltransferase/0.443
3zoiM2WIsopenicillin N synthase1.21.3.10.443
4dfg0JVGag-Pol polyprotein3.4.23.160.443
4f3gKAIGlutamate receptor 3/0.443
1ek2CDUBifunctional epoxide hydrolase 2/0.442
1fm4DXCMajor pollen allergen Bet v 1-L/0.442
1k6vXN2Gag-Pol polyprotein3.4.23.160.442
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1qrpHH0Pepsin A-43.4.23.10.442
1tehNADAlcohol dehydrogenase class-31.1.1.10.442
2bu9HFVIsopenicillin N synthase1.21.3.10.442
2g5cNADPrephenate dehydrogenase/0.442
2xtbKRMAdenosine kinase, putative/0.442
2y0mACOHistone acetyltransferase KAT8/0.442
3dv5BAVBeta-secretase 13.4.23.460.442
3oibFDAPutative acyl-CoA dehydrogenase/0.442
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.442
4g6hNAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.442
4jlm1NNDeoxycytidine kinase2.7.1.740.442
4jq4IMNAldo-keto reductase family 1 member C2/0.442
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.442
4zm6ACON-acetyl-beta-D glucosaminidase/0.442
5cmx0G6Prothrombin3.4.21.50.442
1drhNAPDihydrofolate reductase1.5.1.30.441
1eioGCHGastrotropin/0.441
1i59ADPChemotaxis protein CheA2.7.13.30.441
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.441
1tqf32PBeta-secretase 13.4.23.460.441
1w06W05Isopenicillin N synthase1.21.3.10.441
1ygkRRCPyridoxal kinase2.7.1.350.441
2abbFMNPentaerythritol tetranitrate reductase/0.441
2h8hH8HProto-oncogene tyrosine-protein kinase Src2.7.10.20.441
2igoFADPyranose 2-oxidase/0.441
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.441
2xlpFADPutative flavin-containing monooxygenase/0.441
3dmeFADPutative conserved exported protein/0.441
3zh8C58Protein kinase C iota type2.7.11.130.441
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.441
4lxk1YTBeta-secretase 13.4.23.460.441
1c4yIH3Prothrombin3.4.21.50.440
1dr3HBIDihydrofolate reductase1.5.1.30.440
1fw0KAIGlutamate receptor 2/0.440
1lbbKAIGlutamate receptor 2/0.440
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.440
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.440
1trgCB3Thymidylate synthase/0.440
1w7h3IPMitogen-activated protein kinase 14/0.440
1x8b824Wee1-like protein kinase2.7.10.20.440
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.440
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.440
2pncCLUPrimary amine oxidase, liver isozyme/0.440
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.440
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.440
4cavMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.440
4g1z0VPVitamin D3 receptor A/0.440
4ktl1CQCytochrome P450/0.440
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.440