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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4gt8ADPSensor protein VraS2.7.13.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4gt8ADPSensor protein VraS2.7.13.31.000
1i59ANPChemotaxis protein CheA2.7.13.30.536
2v1aFMNNPH1-1/0.533
5efwFMNNPH1-1/0.507
1thnADPAnti-sigma F factor/0.499
1tilATPAnti-sigma F factor/0.499
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.493
2ejzSAHDiphthine synthase/0.492
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.491
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.486
5dp2NAPCurF/0.485
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.483
1i5aACPChemotaxis protein CheA2.7.13.30.482
2v0uFMNNPH1-1/0.482
4bj9UHBTankyrase-22.4.2.300.482
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.480
4eepFMNPhototropin-22.7.11.10.479
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.478
1g28FMNPHY3/0.477
1i58ACPChemotaxis protein CheA2.7.13.30.477
1lbbKAIGlutamate receptor 2/0.477
2pb4SAHDiphthine synthase/0.477
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
1i59ADPChemotaxis protein CheA2.7.13.30.476
2vbpVB1Isopenicillin N synthase1.21.3.10.473
3gcq1BUMitogen-activated protein kinase 14/0.473
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.473
2yoj8Y6Genome polyprotein2.7.7.480.471
3gb4D3MDdmC/0.471
2c2aADPSensor histidine kinase/0.470
3q9bB3NAcetylpolyamine amidohydrolase/0.470
1pqc444Oxysterols receptor LXR-beta/0.469
2xvv9DNSerum albumin/0.469
3ue6FMNAureochrome1/0.469
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.469
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.467
1nhhANPDNA mismatch repair protein MutL/0.467
1towCRZFatty acid-binding protein, adipocyte/0.466
2emuSAHDiphthine synthase/0.466
4twnB96Ephrin type-A receptor 32.7.10.10.466
2oegUPGUDP-glucose pyrophosphorylase/0.465
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.464
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.464
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.464
3zkyWT4Isopenicillin N synthase1.21.3.10.464
1l0oADPAnti-sigma F factor/0.463
1txtCAAHMG-CoA synthase/0.463
2gjlFMNNitronate monooxygenase1.13.12.160.463
2vcmM11Isopenicillin N synthase1.21.3.10.463
4bftZVTPantothenate kinase2.7.1.330.463
4q71FADBifunctional protein PutA/0.463
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.462
4a862ANMajor pollen allergen Bet v 1-A/0.462
4p9dTMPDeoxycytidylate deaminase/0.461
2y6fM9FIsopenicillin N synthase1.21.3.10.460
3co93MSGenome polyprotein2.7.7.480.460
4a2aATPCell division protein FtsA/0.460
4iz02BIGenome polyprotein2.7.7.480.460
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.460
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.459
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.459
2vczVC3Hematopoietic prostaglandin D synthase/0.459
4fweFADLysine-specific histone demethylase 1B10.459
4wbdADPPutative cysteine ligase BshC/0.459
2he5NDPAldo-keto reductase family 1 member C211.1.10.458
3c36KAIGlutamate receptor ionotropic, kainate 1/0.458
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.458
5iu86DZAdenosine receptor A2a/0.458
2pg0FADAcyl-CoA dehydrogenase/0.457
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3vjcZGASqualene synthase2.5.1.210.457
4a86H35Major pollen allergen Bet v 1-A/0.457
4bfxZVXPantothenate kinase2.7.1.330.457
2y60M8FIsopenicillin N synthase1.21.3.10.456
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.456
1qoqIGPTryptophan synthase alpha chain/0.455
2dv4SAHDiphthine synthase/0.455
3c1oNAPEugenol synthase/0.455
4ocvANPAminoglycoside phosphotransferase/0.455
1h50FMNPentaerythritol tetranitrate reductase/0.454
1i5cADPChemotaxis protein CheA2.7.13.30.454
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.454
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.454
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.454
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.454
3sl2ATPSensor histidine kinase WalK/0.454
4pnmNU1Tankyrase-22.4.2.300.454
1blzACVIsopenicillin N synthase1.21.3.10.453
1dliUDXUDP-glucose 6-dehydrogenase/0.453
1vbiNADMalate/L-lactate dehydrogenase family protein/0.453
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.453
3hl0NADMaleylacetate reductase/0.453
4b66NAPL-ornithine N(5)-monooxygenase/0.453
4bfvZVVPantothenate kinase2.7.1.330.453
4eerFMNPhototropin-22.7.11.10.453
4y1bNAPAntE/0.453
1rxjBNIStreptavidin/0.452
2gjnFMNNitronate monooxygenase1.13.12.160.452
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.452
3b9lAZZSerum albumin/0.452
3e51N35Genome polyprotein2.7.7.480.452
3phjDHKShikimate dehydrogenase (NADP(+))/0.452
1obnASVIsopenicillin N synthase1.21.3.10.451
2bfmTOPPteridine reductase 11.5.1.330.451
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3p0fBAUUridine phosphorylase 22.4.2.30.451
3rsv3RSBeta-secretase 13.4.23.460.451
4b7754MBeta-secretase 13.4.23.460.451
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4xnw2IDP2Y purinoceptor 1/0.451
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.450
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2ea2F77Methionine aminopeptidase 2/0.450
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
5f5rANPHeat shock protein 75 kDa, mitochondrial/0.450
5jtbZMAAdenosine receptor A2a/0.450
2dv5SAHDiphthine synthase/0.449
2wo7ASVIsopenicillin N synthase1.21.3.10.449
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.449
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.449
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.449
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.449
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3hv3R49Mitogen-activated protein kinase 14/0.449
3nmpPYVAbscisic acid receptor PYL2/0.449
3zmg6Z0Beta-secretase 13.4.23.460.449
4epq0RRPoly(ADP-ribose) glycohydrolase/0.449
5djtFMNNPH1-2/0.449
1fw0KAIGlutamate receptor 2/0.448
1pd9CO4Dihydrofolate reductase1.5.1.30.448
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.448
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.448
2geuCOKPantothenate kinase2.7.1.330.448
3s79ASDAromatase1.14.14.140.448
4f3gKAIGlutamate receptor 3/0.448
4gusFADLysine-specific histone demethylase 1B10.448
4jauADPSensor histidine kinase/0.448
4prxADPDNA gyrase subunit B/0.448
3emlZMAAdenosine receptor A2a/0.448
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.447
1touB1VFatty acid-binding protein, adipocyte/0.447
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.447
2cjfRP43-dehydroquinate dehydratase4.2.1.100.447
2uxoTACHTH-type transcriptional regulator TtgR/0.447
1hfqMOTDihydrofolate reductase1.5.1.30.446
1hk4T44Serum albumin/0.446
1kruIPTGalactoside O-acetyltransferase2.3.1.180.446
1s7gNADNAD-dependent protein deacylase 2/0.446
1yqzCOACoenzyme A disulfide reductase/0.446
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.446
3au2DGTDNA polymerase beta family (X family)/0.446
3b05IPEIsopentenyl-diphosphate delta-isomerase/0.446
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3zc3FADFerredoxin--NADP reductase1.18.1.20.446
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.446
4bizADPSensor histidine kinase CpxA/0.446
1e2nRCAThymidine kinase/0.445
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.445
3iktNADRedox-sensing transcriptional repressor Rex/0.445
3vv8B02Beta-secretase 13.4.23.460.445
4uy6SAHHistidine N-alpha-methyltransferase/0.445
5g53NECAdenosine receptor A2a/0.445
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.444
1hb3SCVIsopenicillin N synthase1.21.3.10.444
1pq944BOxysterols receptor LXR-beta/0.444
1t4v14AProthrombin3.4.21.50.444
1yw9A84Methionine aminopeptidase 2/0.444
2fznFADBifunctional protein PutA1.5.5.20.444
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.10.444
2ym1NAPPhenylacetone monooxygenase1.14.13.920.444
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.444
3i0aDBHNeutrophil gelatinase-associated lipocalin/0.444
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.444
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.444
4fwfFADLysine-specific histone demethylase 1B10.444
5k2cZMAAdenosine receptor A2a/0.444
1bmfANPATP synthase subunit alpha, mitochondrial/0.443
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.443
1crbRTLRetinol-binding protein 1/0.443
1qk35GPHypoxanthine-guanine-xanthine phosphoribosyltransferase2.4.2.220.443
1t7o152Carnitine O-acetyltransferase2.3.1.70.443
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.443
4eiyZMAAdenosine receptor A2a/0.443
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.443
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4r39ANPBlue-light-activated histidine kinase 22.7.13.30.443
4ttjFMCPurine nucleoside phosphorylase DeoD-type/0.443
1byqADPHeat shock protein HSP 90-alpha/0.442
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.442
1oc1ASVIsopenicillin N synthase1.21.3.10.442
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.442
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
2rqfJH3Hemolymph juvenile hormone binding protein/0.442
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.442
3i0pNADMalate dehydrogenase, putative/0.442
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.442
3orfNADDihydropteridine reductase1.5.1.340.442
3otwCOAPhosphopantetheine adenylyltransferase/0.442
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.442
4b4vL34Bifunctional protein FolD/0.442
4bekXK0Beta-secretase 13.4.23.460.442
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.442
1lb9DNQGlutamate receptor 2/0.441
1opbRETRetinol-binding protein 2/0.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3t2sAGSHeat shock protein HSP 90-alpha/0.441
3to3ATPPetrobactin biosynthesis protein AsbB/0.441
4xclAGSHeat shock cognate 90 kDa protein/0.441
1hb1OCVIsopenicillin N synthase1.21.3.10.440
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.440
2anmCDOProthrombin3.4.21.50.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2w6pOA4Biotin carboxylase6.3.4.140.440
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.440
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.440
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.440
2yltNAPPhenylacetone monooxygenase1.14.13.920.440
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.440
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3fp0FP015-O-acetyltransferase/0.440
3qgi33FGenome polyprotein2.7.7.480.440
4a802ANMajor pollen allergen Bet v 1-A/0.440
4friDWABeta-secretase 13.4.23.460.440
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.440
5k2aZMAAdenosine receptor A2a/0.440