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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
1ndjBTNStreptavidin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1ndjBTNStreptavidin/1.000
1nc9IMIStreptavidin/0.633
3wypBSOStreptavidin/0.609
2zscBTNTamavidin2/0.600
1swpBTQStreptavidin/0.599
3ry2BTNStreptavidin/0.599
1sreHABStreptavidin/0.591
1n9mBTNStreptavidin/0.590
1mk5BTNStreptavidin/0.587
2fhnBNIAvidin-related protein 4/5/0.586
1stpBTNStreptavidin/0.585
2izfBTNStreptavidin/0.585
4ggzBTNBll1558 protein/0.583
1srgMHBStreptavidin/0.576
4yvbBTNStreptavidin/0.574
1sriDMBStreptavidin/0.572
1swdBTNStreptavidin/0.570
2rtgBTNStreptavidin/0.568
2rtfBTNStreptavidin/0.567
1lcwSHMStreptavidin/0.564
2izkGLLStreptavidin/0.563
4bx7B4FStreptavidin/0.562
2izgBTNStreptavidin/0.560
2rtqIMIStreptavidin/0.558
2izhBTNStreptavidin/0.557
1df8BTNStreptavidin/0.554
1srhMOBStreptavidin/0.550
4gd9BTNStreptavidin/0.550
1avdBTNAvidin/0.549
1luqBTNStreptavidin/0.547
1swtBTNStreptavidin/0.544
2rtrIMIStreptavidin/0.542
2rtiGLLStreptavidin/0.540
2y3fBTNStreptavidin/0.540
4dneDTBStreptavidin/0.537
2rtpIMIStreptavidin/0.536
2izlIMIStreptavidin/0.535
2rtdBTNStreptavidin/0.532
2rtoIMIStreptavidin/0.530
2rteBTNStreptavidin/0.528
1swpBTNStreptavidin/0.526
2rtnIMIStreptavidin/0.526
2rtkGLLStreptavidin/0.524
1rxhBNIStreptavidin/0.521
1srfMTBStreptavidin/0.521
2rtmIMIStreptavidin/0.521
1srjNABStreptavidin/0.520
3wznBTNStreptavidin/0.518
3wyqBTNStreptavidin/0.517
4gdaBTNStreptavidin/0.517
2jgsBTNAvidin/0.515
3vhhVHHAvidin/0.515
1i9hBNIStreptavidin/0.514
3vhmNPKAvidin/0.514
1swnBTNStreptavidin/0.513
1lczBH7Streptavidin/0.512
3vgwNVZAvidin/0.512
2aviBTNAvidin/0.510
3vhiVHIAvidin/0.510
4z28BTNHoefavidin/0.502
3rdqDTBStreptavidin/0.501
2uz2BTNAvd protein/0.500
3t2wBTNAvidin/streptavidin/0.497
2c4iBTNAvidin/0.492
5ch7MD1DMSO reductase family type II enzyme, molybdopterin subunit/0.492
1y52BTNAvidin-related protein 4/5/0.485
2vczVC3Hematopoietic prostaglandin D synthase/0.484
3rbqGLY_ALA_GLY_DAOProtein unc-119 homolog A/0.483
3zkyWT4Isopenicillin N synthase1.21.3.10.482
2wo7ASVIsopenicillin N synthase1.21.3.10.481
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.480
3ew2BTNHypothetical conserved protein/0.480
3h3r14HCollagen type IV alpha-3-binding protein/0.479
5pahLDPPhenylalanine-4-hydroxylase1.14.16.10.479
2fhlBNIAvidin-related protein 4/5/0.478
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.477
3zkuHCVIsopenicillin N synthase1.21.3.10.477
4dvi2IWTankyrase-12.4.2.300.477
5g53NECAdenosine receptor A2a/0.477
2vcmM11Isopenicillin N synthase1.21.3.10.476
3c3xNAPEugenol synthase 11.1.1.3180.475
4pnmNU1Tankyrase-22.4.2.300.475
4bueJQFTankyrase-22.4.2.300.474
4hlf15ZTankyrase-22.4.2.300.474
4l091URTankyrase-22.4.2.300.474
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.472
1hb1OCVIsopenicillin N synthase1.21.3.10.471
3h3qH13Collagen type IV alpha-3-binding protein/0.471
5dp2NAPCurF/0.471
1fvpFMANon-fluorescent flavoprotein/0.470
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.470
1mueCDDProthrombin3.4.21.50.470
2izjBTNStreptavidin/0.470
2bjsACVIsopenicillin N synthase1.21.3.10.469
2iziBTNStreptavidin/0.469
1lkeDOGBilin-binding protein/0.468
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.468
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.468
2fj1CTCTetracycline repressor protein class D/0.468
3bi6396Wee1-like protein kinase2.7.10.20.468
3klbFMNUncharacterized protein/0.467
1obnASVIsopenicillin N synthase1.21.3.10.466
1yryMSGPurine nucleoside phosphorylase2.4.2.10.466
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.466
2qw8NAPEugenol synthase 11.1.1.3180.466
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.466
1oc1ASVIsopenicillin N synthase1.21.3.10.465
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.465
2uywBTNAvd protein/0.465
1bwlFMNNADPH dehydrogenase 11.6.99.10.464
1mvtDTMDihydrofolate reductase1.5.1.30.464
1w6rGNTAcetylcholinesterase3.1.1.70.464
3uic09TEnoyl-[acyl-carrier-protein] reductase [NADH]/0.464
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.464
2vbpVB1Isopenicillin N synthase1.21.3.10.463
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.463
4e32DWNMethyltransferase/0.463
4jtqNAPAldo-keto reductase family 1 member C2/0.463
1d8fSPIStromelysin-13.4.24.170.462
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.462
4bufF36Tankyrase-22.4.2.300.462
4ieiADPGene 2 protein/0.462
1hb3SCVIsopenicillin N synthase1.21.3.10.461
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.461
4b5oACOAlpha-tubulin N-acetyltransferase 1/0.461
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.461
1bx9GLY_GGL_FOEGlutathione S-transferase F22.5.1.180.460
1e2nRCAThymidine kinase/0.460
3d4bDZDNAD-dependent protein deacetylase/0.460
1lnmDTXBilin-binding protein/0.459
1nzq162Prothrombin3.4.21.50.459
1odnAPVIsopenicillin N synthase1.21.3.10.459
1pq944BOxysterols receptor LXR-beta/0.459
1qjfACSIsopenicillin N synthase1.21.3.10.459
2r8pT6FTransketolase 1/0.459
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.458
4buxF35Tankyrase-22.4.2.300.458
4iarERM5-hydroxytryptamine receptor 1B/0.458
4l321VFTankyrase-22.4.2.300.458
4q0kGA3Phytohormone-binding protein/0.458
1blzACVIsopenicillin N synthase1.21.3.10.457
1t4u81AProthrombin3.4.21.50.457
1txtCAAHMG-CoA synthase/0.457
2bfqAR6[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.457
2ea2F77Methionine aminopeptidase 2/0.457
2vbdV10Isopenicillin N synthase1.21.3.10.457
3pahXDEPhenylalanine-4-hydroxylase1.14.16.10.457
4bus32FTankyrase-22.4.2.300.457
1c4uIH1Prothrombin3.4.21.50.456
1mabADPATP synthase subunit beta, mitochondrial3.6.3.140.456
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4f5dC2EStimulator of interferon genes protein/0.456
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.455
2bdyUNBProthrombin3.4.21.50.455
3h3sH15Collagen type IV alpha-3-binding protein/0.455
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.455
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.455
1b3dS27Stromelysin-13.4.24.170.454
1e66HUXAcetylcholinesterase3.1.1.70.454
2bu9HFVIsopenicillin N synthase1.21.3.10.454
2pksG44Prothrombin3.4.21.50.454
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.454
2uuk897Prothrombin3.4.21.50.454
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.454
2xlsFADPutative flavin-containing monooxygenase/0.454
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.454
3iesM24Luciferin 4-monooxygenase1.13.12.70.454
4fhd0TTSpore photoproduct lyase/0.454
4yddMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.454
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.453
3fsjD7KBenzoylformate decarboxylase4.1.1.70.453
3pkbY16Methionine aminopeptidase 2/0.453
3wqmB29Diterpene synthase3.1.7.80.453
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.453
1d9i00PProthrombin3.4.21.50.452
1h22E10Acetylcholinesterase3.1.1.70.452
1u65CP0Acetylcholinesterase3.1.1.70.452
1ut6A8NAcetylcholinesterase3.1.1.70.452
2bjhFERFeruloyl esterase A3.1.1.730.452
3aosJH2Hemolymph juvenile hormone binding protein/0.452
3uxvGUNNADPH-dependent 7-cyano-7-deazaguanine reductase/0.452
4a81DXCMajor pollen allergen Bet v 1-A/0.452
4psbGA3Cytokinin-specific binding protein/0.452
1ecb5GPAmidophosphoribosyltransferase/0.451
1ycgFMNNitric oxide reductase10.451
2ed3SAHDiphthine synthase/0.451
2ejzSAHDiphthine synthase/0.451
2j9lATPH(+)/Cl(-) exchange transporter 5/0.451
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.451
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.451
4fam0SZAldo-keto reductase family 1 member C3/0.451
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.451
1jwtBLIProthrombin3.4.21.50.450
2f0y3MNProtein farnesyltransferase subunit beta2.5.1.580.450
2xlpFADPutative flavin-containing monooxygenase/0.450
3rimTPPTransketolase2.2.1.10.450
4bcsBTNAvidin-related protein 4/5/0.450
4hkkAGITankyrase-22.4.2.300.450
4l1xNAPAldo-keto reductase family 1 member C2/0.450
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.450
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.450
4xnw2IDP2Y purinoceptor 1/0.450
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1isgAGSADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 23.2.2.60.449
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.449
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.449
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.449
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.449
2wnbC5PCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 12.4.99.40.449
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.449
3ngq1PSCCR4-NOT transcription complex subunit 6-like3.1.13.40.449
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
1gveNAPAflatoxin B1 aldehyde reductase member 310.448
1itzTPPTransketolase, chloroplastic2.2.1.10.448
1lquNDPNADPH-ferredoxin reductase FprA1.18.1.20.448
1zgcA2EAcetylcholinesterase3.1.1.70.448
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.448
2zc922UProthrombin3.4.21.50.448
2zhe13UProthrombin3.4.21.50.448
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3eksCY9Actin-5C/0.448
3rnoNAPNAD(P)H-hydrate epimerase5.1.99.60.448
3sfy3FYUncharacterized protein/0.448
3t88S0N1,4-dihydroxy-2-naphthoyl-CoA synthase/0.448
4lcw1VYMajor histocompatibility complex class I-related gene protein/0.448
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.448
4wevSUZAldo-keto reductase family 1 member B101.1.10.448
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.448
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.447
3ko5ADPD-tyrosyl-tRNA(Tyr) deacylase/0.447
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.447
4bb3KKAIsopenicillin N synthase1.21.3.10.447
4hlh20DTankyrase-22.4.2.300.447
1ihiIU5Aldo-keto reductase family 1 member C2/0.446
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.446
1uzwCDHIsopenicillin N synthase1.21.3.10.446
1z7yAA5Cysteine synthase 12.5.1.470.446
2r6jNDPEugenol synthase 11.1.1.3180.446
2xlrFADPutative flavin-containing monooxygenase/0.446
4e2zJHZMethyltransferase/0.446
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.446
4ey6GNTAcetylcholinesterase3.1.1.70.446
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
4phlPILPhosphodiesterase/0.446
4stdBFSScytalone dehydratase4.2.1.940.446
4zwpM44Xaa-Pro dipeptidase3.4.13.90.446
5epoTUD7-alpha-hydroxysteroid deydrogenase/0.446
5fm7ADPRuvB-like helicase/0.446
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.446
1d6w00RProthrombin3.4.21.50.445
1j8uH4BPhenylalanine-4-hydroxylase1.14.16.10.445
2mm3CHOGastrotropin/0.445
2yeiXQIHeat shock protein HSP 90-alpha/0.445
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.445
3q3cNADNAD-dependent L-serine dehydrogenase/0.445
3up0D7SaceDAF-12/0.445
4f0e0RUPoly [ADP-ribose] polymerase 152.4.2.300.445
5iu86DZAdenosine receptor A2a/0.445
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.444
1d3dBZTProthrombin3.4.21.50.444
1h60STRPentaerythritol tetranitrate reductase/0.444
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.444
2flhZEACytokinin-specific binding protein/0.444
2imkGTXAGAP009194-PA/0.444
2xvhFADPutative flavin-containing monooxygenase/0.444
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.444
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.444
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.444
3r43ID8Aldo-keto reductase family 1 member C3/0.444
3wthIM4Acetylcholine-binding protein/0.444
4b1e6T6Beta-secretase 13.4.23.460.444
4bjbP34Tankyrase-22.4.2.300.444
4k4fK4FTankyrase-12.4.2.300.444
4kzl20DTankyrase-22.4.2.300.444
5aku29FTankyrase-22.4.2.300.444
1klkPMDDihydrofolate reductase1.5.1.30.443
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.443
2vqqTFGHistone deacetylase 43.5.1.980.443
2vxkCOAGlucosamine 6-phosphate acetyltransferase, putative/0.443
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
3vjcZGASqualene synthase2.5.1.210.443
4wbdADPPutative cysteine ligase BshC/0.443
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.443
5ilwURIRibosome inactivating protein/0.443
1gjrFADFerredoxin--NADP reductase1.18.1.20.442
1kceCB3Thymidylate synthase/0.442
1mu6CDAProthrombin3.4.21.50.442
1opbRETRetinol-binding protein 2/0.442
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.442
1vzqSHYProthrombin3.4.21.50.442
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.442
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.442
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.442
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3c1kT15Prothrombin3.4.21.50.442
3fhxPLPPyridoxal kinase2.7.1.350.442
3lz6A0DCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3o6o94MHeat shock protein 83/0.442
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.442
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3tm5SFGUncharacterized protein/0.442
4hl1ZZ7Metallo-beta-lactamase type 2/0.442
4rgsV55Repressor protein/0.442
4twnB96Ephrin type-A receptor 32.7.10.10.442
1oytFSNProthrombin3.4.21.50.441
1thnADPAnti-sigma F factor/0.441
1ye6NAPNAD(P)H-dependent D-xylose reductase1.1.1.3070.441
2fzjDH3Dihydrofolate reductase1.5.1.30.441
2r8oT5XTransketolase 1/0.441
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.441
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.441
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.441
3e6eDCSAlanine racemase/0.441
3hy310F5-formyltetrahydrofolate cyclo-ligase6.3.3.20.441
3vmmP0DAlanine--anticapsin ligase/0.441
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.441
4bamMM9Prothrombin3.4.21.50.441
4jq3NAPAldo-keto reductase family 1 member C2/0.441
1dx6GNTAcetylcholinesterase3.1.1.70.440
1g63FMNEpidermin decarboxylase4.1.10.440
1jueFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.440
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.440
2c29NAPDihydroflavonol 4-reductase/0.440
2hq9FADMll6688 protein/0.440
2y6fM9FIsopenicillin N synthase1.21.3.10.440
2zs8ADPPantothenate kinase2.7.1.330.440
3b6pTMPThree-prime repair exonuclease 13.1.11.20.440
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.440
3pkeY10Methionine aminopeptidase 2/0.440
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.440
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.440
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
5ds309LPoly [ADP-ribose] polymerase 12.4.2.300.440
3emlZMAAdenosine receptor A2a/0.440