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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
1ae8AZLProthrombin3.4.21.5

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1ae8AZLProthrombin3.4.21.51.000
1afeALZProthrombin3.4.21.50.825
1d6w00RProthrombin3.4.21.50.726
1t4u81AProthrombin3.4.21.50.693
3eq02TSProthrombin3.4.21.50.688
1mueCDDProthrombin3.4.21.50.687
2zgx29UProthrombin3.4.21.50.685
1k21IGNProthrombin3.4.21.50.671
1t4v14AProthrombin3.4.21.50.669
2zf051UProthrombin3.4.21.50.669
1ypkCCRProthrombin3.4.21.50.666
2zfq45UProthrombin3.4.21.50.666
2zc922UProthrombin3.4.21.50.665
1vzqSHYProthrombin3.4.21.50.663
1ypeUIPProthrombin3.4.21.50.659
2zda32UProthrombin3.4.21.50.656
1zrb062Prothrombin3.4.21.50.655
1d4pBPPProthrombin3.4.21.50.651
2znk31UProthrombin3.4.21.50.651
3dux64UProthrombin3.4.21.50.648
1yplRA8Prothrombin3.4.21.50.647
1sb1165Prothrombin3.4.21.50.646
1mu6CDAProthrombin3.4.21.50.645
3biu10UProthrombin3.4.21.50.645
2v3oI26Prothrombin3.4.21.50.644
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.644
2zi224UProthrombin3.4.21.50.641
4bakM67Prothrombin3.4.21.50.640
1nzq162Prothrombin3.4.21.50.637
1ypjUIBProthrombin3.4.21.50.636
2jh5895Prothrombin3.4.21.50.635
2zfp19UProthrombin3.4.21.50.635
2zg050UProthrombin3.4.21.50.635
1z71L17Prothrombin3.4.21.50.634
2zhf49UProthrombin3.4.21.50.634
2zgb21UProthrombin3.4.21.50.631
2zdv37UProthrombin3.4.21.50.630
2jh6894Prothrombin3.4.21.50.628
2zff53UProthrombin3.4.21.50.627
1d3dBZTProthrombin3.4.21.50.625
2pksG44Prothrombin3.4.21.50.625
3c1kT15Prothrombin3.4.21.50.624
2zfr46UProthrombin3.4.21.50.623
4bamMM9Prothrombin3.4.21.50.623
2anmCDOProthrombin3.4.21.50.621
4ayy9MXProthrombin3.4.21.50.620
2zhe13UProthrombin3.4.21.50.617
1jwtBLIProthrombin3.4.21.50.616
1c4uIH1Prothrombin3.4.21.50.614
1ta6177Prothrombin3.4.21.50.614
4ax9N5NProthrombin3.4.21.50.614
2bvs2CEProthrombin3.4.21.50.613
1bcuPRLProthrombin3.4.21.50.611
1zgv501Prothrombin3.4.21.50.609
2r2mI50Prothrombin3.4.21.50.609
1zgi382Prothrombin3.4.21.50.608
1o5gCR9Prothrombin3.4.21.50.607
2bdyUNBProthrombin3.4.21.50.606
2cf9348Prothrombin3.4.21.50.606
2cf8ESHProthrombin3.4.21.50.603
1c1uBAIProthrombin3.4.21.50.602
1c4yIH3Prothrombin3.4.21.50.602
2uuk897Prothrombin3.4.21.50.602
1ghv120Prothrombin3.4.21.50.601
2cn0F25Prothrombin3.4.21.50.600
1ypmRA4Prothrombin3.4.21.50.599
4lxb7R9Prothrombin3.4.21.50.598
2zhq27UProthrombin3.4.21.50.597
4az29MUProthrombin3.4.21.50.595
1umaIN2Prothrombin3.4.21.50.593
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.592
2uuj896Prothrombin3.4.21.50.589
3qwc98PProthrombin3.4.21.50.589
2zhw12UProthrombin3.4.21.50.587
4ayv9MQProthrombin3.4.21.50.586
1nm6L86Prothrombin3.4.21.50.584
1xm1GAHProthrombin3.4.21.50.584
4e7r0NWProthrombin3.4.21.50.584
4baqM4ZProthrombin3.4.21.50.582
4banM6SProthrombin3.4.21.50.581
1a4wQWEProthrombin3.4.21.50.574
2bxtC2DProthrombin3.4.21.50.574
2gdeSN3Prothrombin3.4.21.50.574
2v3hI25Prothrombin3.4.21.50.573
4bahMELProthrombin3.4.21.50.569
4n3l2FNProthrombin3.4.21.50.564
4baoMVFProthrombin3.4.21.50.562
1c5nESIProthrombin3.4.21.50.555
3p1799PProthrombin3.4.21.50.555
3qto10PProthrombin3.4.21.50.554
1k22MELProthrombin3.4.21.50.550
1riwOSCProthrombin3.4.21.50.547
1w7gMIUProthrombin3.4.21.50.547
3biv11UProthrombin3.4.21.50.547
3c27DKKProthrombin3.4.21.50.547
1c1wBAHProthrombin3.4.21.50.545
1d3pBT3Prothrombin3.4.21.50.545
4rn615UProthrombin3.4.21.50.535
5cmx0G6Prothrombin3.4.21.50.533
3qtv06PProthrombin3.4.21.50.526
1c4vIH2Prothrombin3.4.21.50.524
1gj4132Prothrombin3.4.21.50.524
1o2g696Prothrombin3.4.21.50.523
2ziq26UProthrombin3.4.21.50.516
3utu1TSProthrombin3.4.21.50.516
4loy6XSProthrombin3.4.21.50.515
1o0d163Prothrombin3.4.21.50.514
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.512
1mu8CDBProthrombin3.4.21.50.510
1gj5130Prothrombin3.4.21.50.506
1ta2176Prothrombin3.4.21.50.505
1uvsI11Prothrombin3.4.21.50.502
3f6891UProthrombin3.4.21.50.492
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.490
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.486
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.482
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.482
3adaNADSubunit alpha of sarocosine oxidase/0.480
4hy6FJ1Heat shock protein HSP 90-alpha/0.480
4h1e10JBeta-secretase 13.4.23.460.476
1qoqIGPTryptophan synthase alpha chain/0.473
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.472
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.471
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.471
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.470
2ignFADPyranose 2-oxidase/0.470
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
1mvtDTMDihydrofolate reductase1.5.1.30.466
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.466
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.466
3ihzFK5Peptidylprolyl isomerase/0.466
3o6o94MHeat shock protein 83/0.466
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.466
1p0pBCHCholinesterase3.1.1.80.465
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
4q71FADBifunctional protein PutA/0.464
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.463
4zj8SUVOrexin receptor type 1/0.463
1pq944BOxysterols receptor LXR-beta/0.462
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.461
3vqsJT1Genome polyprotein/0.460
4dc0NDPPutative ketoacyl reductase1.3.10.460
4gxs0YSGlutamate receptor 2/0.460
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.459
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.459
4kbyC2EStimulator of interferon genes protein/0.459
3nmpPYVAbscisic acid receptor PYL2/0.458
1nytNAPShikimate dehydrogenase (NADP(+))/0.457
4c717RD3-oxoacyl-ACP synthase/0.456
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.456
2e7rSAHDiphthine synthase/0.455
4uugPXGBranched-chain amino acid aminotransferase, putative/0.455
2p2xSAHDiphthine synthase/0.454
2xuhTZ4Acetylcholinesterase3.1.1.70.454
3wtkTH4Acetylcholine-binding protein/0.454
2e94364Geranylgeranyl pyrophosphate synthase/0.453
2geuCOKPantothenate kinase2.7.1.330.453
3qgf46FGenome polyprotein2.7.7.480.453
3v76FDAUncharacterized protein/0.453
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.453
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.453
1s3uTQDDihydrofolate reductase1.5.1.30.452
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.452
3k1wBFXRenin3.4.23.150.452
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.451
1vi2NADQuinate/shikimate dehydrogenase/0.451
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.451
4b1jA1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.451
4jeyPLPAcetylornithine/succinyldiaminopimelate aminotransferase2.6.1.110.451
1o9bNAIQuinate/shikimate dehydrogenase/0.450
1pqc444Oxysterols receptor LXR-beta/0.450
2xufTZ4Acetylcholinesterase3.1.1.70.450
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
4qii2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.450
1hf3NADAlcohol dehydrogenase E chain1.1.1.10.449
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
3gkjHC3Niemann-Pick C1 protein/0.449
1bpwNADBetaine aldehyde dehydrogenase1.2.1.80.448
2fonFADAcyl-coenzyme A oxidase/0.448
4fam0SZAldo-keto reductase family 1 member C3/0.448
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.448
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.447
1q84TZ4Acetylcholinesterase3.1.1.70.447
2y37A54Nitric oxide synthase, inducible1.14.13.390.447
3ha5SFGHydroxymycolate synthase MmaA42.1.10.447
3qrwNDPPutative ketoacyl reductase1.3.10.447
1eioGCHGastrotropin/0.446
1x7hNDPPutative ketoacyl reductase1.3.10.446
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.446
2yeiXQIHeat shock protein HSP 90-alpha/0.446
2yk2YJWHeat shock protein HSP 90-alpha/0.446
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4h6pFMNChromate reductase/0.446
4k2xFADPolyketide oxygenase/hydroxylase/0.446
1zgcA2EAcetylcholinesterase3.1.1.70.445
2p5cSAHDiphthine synthase/0.445
3c1oNAPEugenol synthase/0.445
4bfxZVXPantothenate kinase2.7.1.330.445
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.444
1pw1HELD-alanyl-D-alanine carboxypeptidase3.4.16.40.444
2dvlFADAcyl-CoA dehydrogenase/0.444
2pg0FADAcyl-CoA dehydrogenase/0.444
2z52H23Geranylgeranyl pyrophosphate synthase/0.444
4frkDWDBeta-secretase 13.4.23.460.444
4mihFADPyranose 2-oxidase1.1.3.100.444
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.443
1ktsC24Prothrombin3.4.21.50.443
1upw444Oxysterols receptor LXR-beta/0.443
3q7fED2Uncharacterized protein/0.443
4b45GSPTubulin-like protein CetZ2/0.443
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.442
2f3815MAldo-keto reductase family 1 member C3/0.442
2j3qTFLAcetylcholinesterase3.1.1.70.442
2wf1ZY1Beta-secretase 13.4.23.460.442
2zevIPEGeranylgeranyl pyrophosphate synthase/0.442
3hxbBD5Geranylgeranyl transferase type-2 subunit beta2.5.1.600.442
3rsv3RSBeta-secretase 13.4.23.460.442
3sjuNDPKeto reductase/0.442
4ktkKTKCytochrome P450/0.442
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.441
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.441
2r5nTPPTransketolase 1/0.441
2vkeTACTetracycline repressor protein class D/0.441
2xukTZ5Acetylcholinesterase3.1.1.70.441
2yee2ECHeat shock protein HSP 90-alpha/0.441
2ykjYKJHeat shock protein HSP 90-alpha/0.441
3akzGSUGlutamate--tRNA ligase 2/0.441
3c35KAIGlutamate receptor ionotropic, kainate 1/0.441
3d91REMRenin3.4.23.150.441
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3otwCOAPhosphopantetheine adenylyltransferase/0.441
3uxvGUNNADPH-dependent 7-cyano-7-deazaguanine reductase/0.441
3zkuHCVIsopenicillin N synthase1.21.3.10.441
4acuQN7Beta-secretase 13.4.23.460.441
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.441
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
4dc1NDPPutative ketoacyl reductase1.3.10.441
1mvsDTMDihydrofolate reductase1.5.1.30.440
1uycPU7Heat shock protein HSP 90-alpha/0.440
2ckmAA7Acetylcholinesterase3.1.1.70.440
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.440
2fs4PZ1Renin3.4.23.150.440
3gwfFADCyclohexanone monooxygenase/0.440
4a802ANMajor pollen allergen Bet v 1-A/0.440
4yryFADGlutamate synthase, beta subunit/0.440
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.440