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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
1c4vIH2Prothrombin3.4.21.5

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1c4vIH2Prothrombin3.4.21.51.000
1gj5130Prothrombin3.4.21.50.685
1d3pBT3Prothrombin3.4.21.50.678
1ypmRA4Prothrombin3.4.21.50.668
2anmCDOProthrombin3.4.21.50.667
1o2g696Prothrombin3.4.21.50.665
2zhf49UProthrombin3.4.21.50.664
2r2mI50Prothrombin3.4.21.50.659
2bdyUNBProthrombin3.4.21.50.656
1d3dBZTProthrombin3.4.21.50.652
1ghv120Prothrombin3.4.21.50.652
3qwc98PProthrombin3.4.21.50.652
1ypjUIBProthrombin3.4.21.50.651
2zhq27UProthrombin3.4.21.50.647
1ta6177Prothrombin3.4.21.50.632
1mu8CDBProthrombin3.4.21.50.629
1xm1GAHProthrombin3.4.21.50.629
2zda32UProthrombin3.4.21.50.629
2zhe13UProthrombin3.4.21.50.629
2zfp19UProthrombin3.4.21.50.628
1c5nESIProthrombin3.4.21.50.626
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.625
1c4uIH1Prothrombin3.4.21.50.621
1d4pBPPProthrombin3.4.21.50.621
1gj4132Prothrombin3.4.21.50.621
2jh5895Prothrombin3.4.21.50.621
2zhw12UProthrombin3.4.21.50.621
2v3oI26Prothrombin3.4.21.50.620
2cn0F25Prothrombin3.4.21.50.617
2bvs2CEProthrombin3.4.21.50.616
1d9i00PProthrombin3.4.21.50.614
2jh6894Prothrombin3.4.21.50.611
2cf8ESHProthrombin3.4.21.50.610
3c1kT15Prothrombin3.4.21.50.610
3dhk23UProthrombin3.4.21.50.610
1sb1165Prothrombin3.4.21.50.609
2a2xNA9Prothrombin3.4.21.50.609
2zdv37UProthrombin3.4.21.50.607
1bcuPRLProthrombin3.4.21.50.606
1yplRA8Prothrombin3.4.21.50.605
2uuk897Prothrombin3.4.21.50.604
1oytFSNProthrombin3.4.21.50.603
1mu6CDAProthrombin3.4.21.50.602
1t4v14AProthrombin3.4.21.50.600
2zgx29UProthrombin3.4.21.50.600
2zg050UProthrombin3.4.21.50.599
1ypeUIPProthrombin3.4.21.50.596
3biu10UProthrombin3.4.21.50.596
1ktsC24Prothrombin3.4.21.50.594
3egkM18Prothrombin3.4.21.50.594
4lxb7R9Prothrombin3.4.21.50.594
2zc922UProthrombin3.4.21.50.593
4ayy9MXProthrombin3.4.21.50.593
1z71L17Prothrombin3.4.21.50.592
2pksG44Prothrombin3.4.21.50.592
1zgi382Prothrombin3.4.21.50.591
2zgb21UProthrombin3.4.21.50.587
1o0d163Prothrombin3.4.21.50.586
2zi224UProthrombin3.4.21.50.585
1umaIN2Prothrombin3.4.21.50.584
4hfp15UProthrombin3.4.21.50.584
1t4u81AProthrombin3.4.21.50.583
2jh0701Prothrombin3.4.21.50.583
2cf9348Prothrombin3.4.21.50.582
3eq02TSProthrombin3.4.21.50.582
4loy6XSProthrombin3.4.21.50.580
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.577
2ziq26UProthrombin3.4.21.50.577
1nzq162Prothrombin3.4.21.50.576
2zfq45UProthrombin3.4.21.50.574
1o5gCR9Prothrombin3.4.21.50.572
1uvsI11Prothrombin3.4.21.50.571
3dux64UProthrombin3.4.21.50.562
2znk31UProthrombin3.4.21.50.559
1jwtBLIProthrombin3.4.21.50.558
1zgv501Prothrombin3.4.21.50.556
1d6w00RProthrombin3.4.21.50.555
1ypgUIRProthrombin3.4.21.50.554
1mueCDDProthrombin3.4.21.50.551
1ypkCCRProthrombin3.4.21.50.549
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.548
3biv11UProthrombin3.4.21.50.547
1ae8AZLProthrombin3.4.21.50.546
2v3hI25Prothrombin3.4.21.50.546
1riwOSCProthrombin3.4.21.50.542
2gdeSN3Prothrombin3.4.21.50.538
3p1799PProthrombin3.4.21.50.538
3f6891UProthrombin3.4.21.50.535
3qto10PProthrombin3.4.21.50.534
4e7r0NWProthrombin3.4.21.50.533
1k21IGNProthrombin3.4.21.50.532
4bamMM9Prothrombin3.4.21.50.532
4baoMVFProthrombin3.4.21.50.532
3c27DKKProthrombin3.4.21.50.530
1zrb062Prothrombin3.4.21.50.527
3qtv06PProthrombin3.4.21.50.521
1vzqSHYProthrombin3.4.21.50.518
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.517
4ayv9MQProthrombin3.4.21.50.515
5cmx0G6Prothrombin3.4.21.50.515
4az29MUProthrombin3.4.21.50.511
4rn615UProthrombin3.4.21.50.507
4bakM67Prothrombin3.4.21.50.500
1c4yIH3Prothrombin3.4.21.50.498
1owe675Urokinase-type plasminogen activator3.4.21.730.494
1ta2176Prothrombin3.4.21.50.493
2uuj896Prothrombin3.4.21.50.492
1afeALZProthrombin3.4.21.50.491
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.489
3utu1TSProthrombin3.4.21.50.487
3v0xANHCationic trypsin3.4.21.40.487
1c1uBAIProthrombin3.4.21.50.483
1zsk421Coagulation factor XI3.4.21.270.481
2hxzH7JCathepsin S3.4.22.270.477
1a4wQWEProthrombin3.4.21.50.476
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.476
4fuiUI3Urokinase-type plasminogen activator3.4.21.730.475
1w7gMIUProthrombin3.4.21.50.474
1sqtUI3Urokinase-type plasminogen activator3.4.21.730.473
1oc1ASVIsopenicillin N synthase1.21.3.10.470
4esoNAPPutative oxidoreductase/0.470
2vivVG2Urokinase-type plasminogen activator3.4.21.730.469
3q9bB3NAcetylpolyamine amidohydrolase/0.469
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.468
2x9dITCTetracycline repressor protein class D/0.468
1dr5NAPDihydrofolate reductase1.5.1.30.466
2xukTZ5Acetylcholinesterase3.1.1.70.466
4fuf8UPUrokinase-type plasminogen activator3.4.21.730.466
1qiqACCIsopenicillin N synthase1.21.3.10.465
2g004QCCoagulation factor X3.4.21.60.465
2nr4FMNConserved protein/0.465
2gjlFMNNitronate monooxygenase1.13.12.160.464
3fhxPXLPyridoxal kinase2.7.1.350.464
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.464
4fam0SZAldo-keto reductase family 1 member C3/0.464
3zoiM2WIsopenicillin N synthase1.21.3.10.463
1wqvPSMCoagulation factor VII3.4.21.210.461
2e94364Geranylgeranyl pyrophosphate synthase/0.461
4bfxZVXPantothenate kinase2.7.1.330.461
4q71FADBifunctional protein PutA/0.461
1iqeXMBCoagulation factor X3.4.21.60.460
2vcmM11Isopenicillin N synthase1.21.3.10.459
4banM6SProthrombin3.4.21.50.459
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3fhxPLPPyridoxal kinase2.7.1.350.458
3oafOAGDihydrofolate reductase1.5.1.30.458
4brdANPEctonucleoside triphosphate diphosphohydrolase I/0.458
4fue7UPUrokinase-type plasminogen activator3.4.21.730.458
4i101BSBeta-secretase 13.4.23.460.458
4m6jNDPDihydrofolate reductase1.5.1.30.458
4baqM4ZProthrombin3.4.21.50.457
4c717RD3-oxoacyl-ACP synthase/0.457
4df2FMNNADPH dehydrogenase/0.457
1dhfFOLDihydrofolate reductase1.5.1.30.456
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.456
4fud6UPUrokinase-type plasminogen activator3.4.21.730.456
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.455
3tozNADShikimate dehydrogenase (NADP(+))/0.455
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
1b2lNDCAlcohol dehydrogenase1.1.1.10.454
1towCRZFatty acid-binding protein, adipocyte/0.454
4kbyC2EStimulator of interferon genes protein/0.454
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.454
1ikiREYD-alanyl-D-alanine carboxypeptidase3.4.16.40.453
1p0pBCHCholinesterase3.1.1.80.453
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3n0hTOPDihydrofolate reductase1.5.1.30.453
1obnASVIsopenicillin N synthase1.21.3.10.451
2bu9HFVIsopenicillin N synthase1.21.3.10.451
2rqfJH3Hemolymph juvenile hormone binding protein/0.451
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.450
2zcvNDPQuinone oxidoreductase 21.6.5.20.450
3hk1B64Fatty acid-binding protein, adipocyte/0.450
1h65GDPTranslocase of chloroplast 343.6.50.449
1iqgXMECoagulation factor X3.4.21.60.449
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.449
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.448
2fznFADBifunctional protein PutA1.5.5.20.448
2vkeTACTetracycline repressor protein class D/0.448
2z4y252Geranylgeranyl pyrophosphate synthase/0.448
3juqAJDPhenazine biosynthesis protein A/B/0.448
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
4jlm1NNDeoxycytidine kinase2.7.1.740.448
2bxoOPBSerum albumin/0.447
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.447
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.447
1blzACVIsopenicillin N synthase1.21.3.10.446
1dr3TAPDihydrofolate reductase1.5.1.30.446
1pd9CO4Dihydrofolate reductase1.5.1.30.446
1rkwPNTHTH-type transcriptional regulator QacR/0.446
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.446
2fahGDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial4.1.1.320.446
2g1n1IGRenin3.4.23.150.446
3fr28CAFatty acid-binding protein, adipocyte/0.446
3vydVYDRenin3.4.23.150.446
1hb3SCVIsopenicillin N synthase1.21.3.10.445
1vja7INUrokinase-type plasminogen activator3.4.21.730.445
3p2oNADBifunctional protein FolD/0.445
4g8jTHMUridine phosphorylase/0.445
4j6bPLOCytochrome P450 monooxygenase/0.445
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.445
1rpwDIDHTH-type transcriptional regulator QacR/0.444
2gv8NDPThiol-specific monooxygenase1.14.130.444
2vbdV10Isopenicillin N synthase1.21.3.10.444
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3e2sFADBifunctional protein PutA1.5.5.20.444
3mauPLRPutative sphingosine-1-phosphate lyase/0.444
4a802ANMajor pollen allergen Bet v 1-A/0.444
4bfsZVSPantothenate kinase2.7.1.330.444
4bfuZVUPantothenate kinase2.7.1.330.444
4g95OAGDihydrofolate reductase1.5.1.30.444
1drhNAPDihydrofolate reductase1.5.1.30.443
1enpNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.443
2a2sGSNGlutathione S-transferase P2.5.1.180.443
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2fzmFADBifunctional protein PutA1.5.5.20.443
2v13C40Renin3.4.23.150.443
3aezGDPPantothenate kinase2.7.1.330.443
3cb2GDPTubulin gamma-1 chain/0.443
4c73TLH3-oxoacyl-ACP synthase/0.443
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4ey6GNTAcetylcholinesterase3.1.1.70.443
1cneFADNitrate reductase [NADH]1.7.1.10.442
1cnfFADNitrate reductase [NADH]1.7.1.10.442
1owk303Urokinase-type plasminogen activator3.4.21.730.442
1qjfACSIsopenicillin N synthase1.21.3.10.442
1qoqIGPTryptophan synthase alpha chain/0.442
1yqsBSAD-alanyl-D-alanine carboxypeptidase3.4.16.40.442
2ejzSAHDiphthine synthase/0.442
2geuCOKPantothenate kinase2.7.1.330.442
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3fp0FP015-O-acetyltransferase/0.442
3t4hMD5Alpha-ketoglutarate-dependent dioxygenase AlkB1.14.11.330.442
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.442
5dp2NAPCurF/0.442
1ra3MTXDihydrofolate reductase1.5.1.30.441
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
2b9yFADPutative aminooxidase/0.441
2xugTZ4Acetylcholinesterase3.1.1.70.441
2zp0PI0Coagulation factor VII3.4.21.210.441
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.441
3h3qH13Collagen type IV alpha-3-binding protein/0.441
3wqmB29Diterpene synthase3.1.7.80.441
3zkyWT4Isopenicillin N synthase1.21.3.10.441
4btu6XSCoagulation factor X3.4.21.60.441
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.441
5c1d12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.441
1esmCOAPantothenate kinase2.7.1.330.440
1f92UKPUrokinase-type plasminogen activator3.4.21.730.440
1ptjNAPNAD(P) transhydrogenase subunit beta1.6.1.20.440
1sl3170Prothrombin3.4.21.50.440
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
2y5gFJDCoagulation factor X3.4.21.60.440
3dziRGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.440
3junAJDPhenazine biosynthesis protein A/B/0.440
3v2uATPProtein GAL3/0.440
4b1c1B1Beta-secretase 13.4.23.460.440
4c3yANB3-ketosteroid dehydrogenase/0.440
4kne1CYDihydrofolate reductase1.5.1.30.440
5bqfNAPProbable hydroxyacid dehydrogenase protein/0.440