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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
4gt8ADPSensor protein VraS2.7.13.3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4gt8ADPSensor protein VraS2.7.13.31.000
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.538
1i59ANPChemotaxis protein CheA2.7.13.30.536
3ehjACPSensor histidine kinase DesK2.7.13.30.535
2v1aFMNNPH1-1/0.533
3gieACPSensor histidine kinase DesK2.7.13.30.523
5efwFMNNPH1-1/0.507
2ejzSAHDiphthine synthase/0.504
1thnADPAnti-sigma F factor/0.500
1tilATPAnti-sigma F factor/0.500
1i5bANPChemotaxis protein CheA2.7.13.30.499
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.495
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.495
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.493
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.488
5dp2NAPCurF/0.488
1pvgANPDNA topoisomerase 25.99.1.30.487
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.484
4bj9UHBTankyrase-22.4.2.300.483
1i5aACPChemotaxis protein CheA2.7.13.30.482
2v0uFMNNPH1-1/0.482
1vbiNADMalate/L-lactate dehydrogenase family protein/0.481
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
1pqc444Oxysterols receptor LXR-beta/0.480
2vbpVB1Isopenicillin N synthase1.21.3.10.480
3ske054Genome polyprotein2.7.7.480.480
2yoj8Y6Genome polyprotein2.7.7.480.479
4eepFMNPhototropin-22.7.11.10.479
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.478
1i58ACPChemotaxis protein CheA2.7.13.30.478
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.478
1g28FMNPHY3/0.477
3gb4D3MDdmC/0.477
3gcq1BUMitogen-activated protein kinase 14/0.477
1i59ADPChemotaxis protein CheA2.7.13.30.476
3ue6FMNAureochrome1/0.476
3zkyWT4Isopenicillin N synthase1.21.3.10.476
2pb4SAHDiphthine synthase/0.475
1hb1OCVIsopenicillin N synthase1.21.3.10.473
2c2aADPSensor histidine kinase/0.472
2oegUPGUDP-glucose pyrophosphorylase/0.471
3uph0C1Genome polyprotein2.7.7.480.471
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.471
3q9bB3NAcetylpolyamine amidohydrolase/0.470
4bftZVTPantothenate kinase2.7.1.330.470
1hb3SCVIsopenicillin N synthase1.21.3.10.469
2xvv9DNSerum albumin/0.469
2y60M8FIsopenicillin N synthase1.21.3.10.469
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.469
1l0oADPAnti-sigma F factor/0.468
1nhhANPDNA mismatch repair protein MutL/0.468
1qjfACSIsopenicillin N synthase1.21.3.10.467
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
2gc8885Polyprotein/0.467
4twnB96Ephrin type-A receptor 32.7.10.10.467
1towCRZFatty acid-binding protein, adipocyte/0.466
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.466
1obnASVIsopenicillin N synthase1.21.3.10.465
3co93MSGenome polyprotein2.7.7.480.465
3sl2ATPSensor histidine kinase WalK/0.465
4q71FADBifunctional protein PutA/0.465
5dozNDPJamJ/0.465
2emuSAHDiphthine synthase/0.464
2iviACWIsopenicillin N synthase1.21.3.10.464
2vcmM11Isopenicillin N synthase1.21.3.10.464
2y6fM9FIsopenicillin N synthase1.21.3.10.464
3hl0NADMaleylacetate reductase/0.464
4bfxZVXPantothenate kinase2.7.1.330.464
1bk0ACVIsopenicillin N synthase1.21.3.10.463
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.463
1txtCAAHMG-CoA synthase/0.463
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.463
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.462
4a2aATPCell division protein FtsA/0.462
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.462
4wbdADPPutative cysteine ligase BshC/0.462
2xvw9NRSerum albumin/0.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.461
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.460
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
4iz02BIGenome polyprotein2.7.7.480.460
1lbbKAIGlutamate receptor 2/0.459
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.459
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.459
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.459
2dv5SAHDiphthine synthase/0.459
4a86H35Major pollen allergen Bet v 1-A/0.459
1blzACVIsopenicillin N synthase1.21.3.10.458
1oc1ASVIsopenicillin N synthase1.21.3.10.458
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.458
3b9lAZZSerum albumin/0.458
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.458
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
4ocvANPAminoglycoside phosphotransferase/0.458
1dliUDXUDP-glucose 6-dehydrogenase/0.457
2he5NDPAldo-keto reductase family 1 member C211.1.10.457
2pg0FADAcyl-CoA dehydrogenase/0.457
3csoXNIGenome polyprotein2.7.7.480.457
1i5cADPChemotaxis protein CheA2.7.13.30.456
1pd9CO4Dihydrofolate reductase1.5.1.30.456
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.456
3af1GDPPantothenate kinase2.7.1.330.456
4bfvZVVPantothenate kinase2.7.1.330.456
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.456
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
1z5aADPType 2 DNA topoisomerase 6 subunit B/0.455
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.455
4y1bNAPAntE/0.455
5esdTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.455
5g53NECAdenosine receptor A2a/0.455
5iu86DZAdenosine receptor A2a/0.455
1rxjBNIStreptavidin/0.454
1yqzCOACoenzyme A disulfide reductase/0.454
4bb3KKAIsopenicillin N synthase1.21.3.10.454
4eerFMNPhototropin-22.7.11.10.454
4fweFADLysine-specific histone demethylase 1B10.454
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.453
2jb4A14Isopenicillin N synthase1.21.3.10.453
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.453
3bi6396Wee1-like protein kinase2.7.10.20.453
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3uk6ADPRuvB-like 23.6.4.120.453
4b66NAPL-ornithine N(5)-monooxygenase/0.453
4epq0RRPoly(ADP-ribose) glycohydrolase/0.453
4xq9NADHomospermidine synthase2.5.1.440.453
1kruIPTGalactoside O-acetyltransferase2.3.1.180.452
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.452
1s7gNADNAD-dependent protein deacylase 2/0.452
1w7h3IPMitogen-activated protein kinase 14/0.452
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.452
2bfmTOPPteridine reductase 11.5.1.330.452
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.452
2wo7ASVIsopenicillin N synthase1.21.3.10.452
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.452
2vczVC3Hematopoietic prostaglandin D synthase/0.451
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.451
3e51N35Genome polyprotein2.7.7.480.451
3hv3R49Mitogen-activated protein kinase 14/0.451
4pnmNU1Tankyrase-22.4.2.300.451
5f5rANPHeat shock protein 75 kDa, mitochondrial/0.451
1gpnHUBAcetylcholinesterase3.1.1.70.450
2ea2F77Methionine aminopeptidase 2/0.450
2vd0D27Hematopoietic prostaglandin D synthase/0.450
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.450
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.450
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.450
4b722FBBeta-secretase 13.4.23.460.450
4gusFADLysine-specific histone demethylase 1B10.450
4mka2AYGenome polyprotein2.7.7.480.450
4ttjFMCPurine nucleoside phosphorylase DeoD-type/0.450
4xnw2IDP2Y purinoceptor 1/0.450
1e2nRCAThymidine kinase/0.449
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.449
1touB1VFatty acid-binding protein, adipocyte/0.449
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.449
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.449
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.449
2x7hPFNProstaglandin reductase 310.449
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3p0fBAUUridine phosphorylase 22.4.2.30.449
4b68NAPL-ornithine N(5)-monooxygenase/0.449
4cdmFO1Deoxyribodipyrimidine photolyase/0.449
4mk728OGenome polyprotein2.7.7.480.449
4prxADPDNA gyrase subunit B/0.449
5djtFMNNPH1-2/0.449
1hfqMOTDihydrofolate reductase1.5.1.30.448
2cjfRP43-dehydroquinate dehydratase4.2.1.100.448
2geuCOKPantothenate kinase2.7.1.330.448
2w6pOA4Biotin carboxylase6.3.4.140.448
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.448
3c36KAIGlutamate receptor ionotropic, kainate 1/0.448
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.448
3vv8B02Beta-secretase 13.4.23.460.448
3zoiM2WIsopenicillin N synthase1.21.3.10.448
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.448
4bfwZVWPantothenate kinase2.7.1.330.448
4bizADPSensor histidine kinase CpxA/0.448
4jauADPSensor histidine kinase/0.448
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.448
1hk4T44Serum albumin/0.447
2ed3SAHDiphthine synthase/0.447
2g8yNADHydroxycarboxylate dehydrogenase B/0.447
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3rsv3RSBeta-secretase 13.4.23.460.447
3zmg6Z0Beta-secretase 13.4.23.460.447
4xrgNADHomospermidine synthase2.5.1.440.447
1k7fIAVTryptophan synthase alpha chain/0.446
2dv4SAHDiphthine synthase/0.446
2xszATPRuvB-like 23.6.4.120.446
3orfNADDihydropteridine reductase1.5.1.340.446
3pqbVGPPutative oxidoreductase/0.446
3zc3FADFerredoxin--NADP reductase1.18.1.20.446
4bekXK0Beta-secretase 13.4.23.460.446
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
1ay0TPPTransketolase 12.2.1.10.445
1c4yIH3Prothrombin3.4.21.50.445
2gfsPQBMitogen-activated protein kinase 14/0.445
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
2rgoFADAlpha-Glycerophosphate Oxidase/0.445
3af3GCPPantothenate kinase2.7.1.330.445
3c35KAIGlutamate receptor ionotropic, kainate 1/0.445
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4ih71ERGenome polyprotein2.7.7.480.445
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.445
4ybnFADFlavin-nucleotide-binding protein/0.445
1crbRTLRetinol-binding protein 1/0.444
1gsfEAAGlutathione S-transferase A12.5.1.180.444
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1uzwCDHIsopenicillin N synthase1.21.3.10.444
1yw9A84Methionine aminopeptidase 2/0.444
2bakAQZMitogen-activated protein kinase 14/0.444
2bu9HFVIsopenicillin N synthase1.21.3.10.444
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
2fznFADBifunctional protein PutA1.5.5.20.444
2v59LZKBiotin carboxylase6.3.4.140.444
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.444
4a9yAQZMitogen-activated protein kinase 14/0.444
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.444
5ej7TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.444
1fw0KAIGlutamate receptor 2/0.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
1qk35GPHypoxanthine-guanine-xanthine phosphoribosyltransferase2.4.2.220.443
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.443
2p5cSAHDiphthine synthase/0.443
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.443
2ydoADNAdenosine receptor A2a/0.443
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.443
3ska053Genome polyprotein2.7.7.480.443
4b65NDPL-ornithine N(5)-monooxygenase/0.443
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.443
4r39ANPBlue-light-activated histidine kinase 22.7.13.30.443
4v12POGMaoC like domain protein/0.443
1byqADPHeat shock protein HSP 90-alpha/0.442
1h50FMNPentaerythritol tetranitrate reductase/0.442
1qrsATPGlutamine--tRNA ligase6.1.1.180.442
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.442
1rd7FOLDihydrofolate reductase1.5.1.30.442
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2gv8NDPThiol-specific monooxygenase1.14.130.442
2rqfJH3Hemolymph juvenile hormone binding protein/0.442
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
3d4bDZDNAD-dependent protein deacetylase/0.442
3hz137DHeat shock protein HSP 90-alpha/0.442
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.442
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4h3j10WBeta-secretase 13.4.23.460.442
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.442
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.442
4xclAGSHeat shock cognate 90 kDa protein/0.442
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.441
1x8lOXRRetinol dehydratase/0.441
1xe55FEPlasmepsin-23.4.23.390.441
2qe2452Polyprotein/0.441
3g86T18Genome polyprotein2.7.7.480.441
3h3qH13Collagen type IV alpha-3-binding protein/0.441
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.441
3t2sAGSHeat shock protein HSP 90-alpha/0.441
3uyk0CXProbable NDP-rhamnosyltransferase/0.441
4a7b3W4Collagenase 33.4.240.441
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.441
5ig2NADShort-chain dehydrogenase/reductase SDR/0.441
1drhNAPDihydrofolate reductase1.5.1.30.440
1enoNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.440
1gvhFADFlavohemoprotein/0.440
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.440
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.440
2a9y26AAdenosine kinase2.7.1.200.440
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.440
2po7CHDFerrochelatase, mitochondrial4.99.1.10.440
2zryFNRIsopentenyl-diphosphate delta-isomerase/0.440
3a1l2CCCytochrome P450/0.440
3gqzGF7Beta-lactamase3.5.2.60.440
3iktNADRedox-sensing transcriptional repressor Rex/0.440
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.440
3wv9FEGHmd co-occurring protein HcgE/0.440
4biwANPSensor histidine kinase CpxA/0.440
4edz0O5Hematopoietic prostaglandin D synthase/0.440
4fwfFADLysine-specific histone demethylase 1B10.440
4fxfATPPyruvate kinase PKM2.7.1.400.440
4plpNADHomospermidine synthase2.5.1.440.440
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440