Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3biv11UProthrombin3.4.21.5

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3biv11UProthrombin3.4.21.51.000
2znk31UProthrombin3.4.21.50.865
2zdv37UProthrombin3.4.21.50.846
2zg050UProthrombin3.4.21.50.825
2zda32UProthrombin3.4.21.50.817
2zgx29UProthrombin3.4.21.50.807
3biu10UProthrombin3.4.21.50.792
2ziq26UProthrombin3.4.21.50.778
2zfq45UProthrombin3.4.21.50.777
2zff53UProthrombin3.4.21.50.772
2zhf49UProthrombin3.4.21.50.765
2zc922UProthrombin3.4.21.50.759
2zfr46UProthrombin3.4.21.50.752
2zhe13UProthrombin3.4.21.50.752
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.737
4ax9N5NProthrombin3.4.21.50.725
3dhk23UProthrombin3.4.21.50.723
3dux64UProthrombin3.4.21.50.710
3eq02TSProthrombin3.4.21.50.706
2zhq27UProthrombin3.4.21.50.703
4bamMM9Prothrombin3.4.21.50.702
2zgb21UProthrombin3.4.21.50.692
2zf051UProthrombin3.4.21.50.669
1mueCDDProthrombin3.4.21.50.666
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.664
2zfp19UProthrombin3.4.21.50.655
1zrb062Prothrombin3.4.21.50.653
1d6w00RProthrombin3.4.21.50.650
1ypgUIRProthrombin3.4.21.50.649
4bakM67Prothrombin3.4.21.50.645
2r2mI50Prothrombin3.4.21.50.643
3f6891UProthrombin3.4.21.50.641
1ypkCCRProthrombin3.4.21.50.638
1afeALZProthrombin3.4.21.50.628
1k21IGNProthrombin3.4.21.50.628
1t4v14AProthrombin3.4.21.50.628
1yplRA8Prothrombin3.4.21.50.627
2bvs2CEProthrombin3.4.21.50.627
3egkM18Prothrombin3.4.21.50.627
2jh5895Prothrombin3.4.21.50.625
1d4pBPPProthrombin3.4.21.50.624
1mu8CDBProthrombin3.4.21.50.621
1o0d163Prothrombin3.4.21.50.620
1ae8AZLProthrombin3.4.21.50.618
3qwc98PProthrombin3.4.21.50.617
1sb1165Prothrombin3.4.21.50.615
1z71L17Prothrombin3.4.21.50.615
3c1kT15Prothrombin3.4.21.50.615
2jh6894Prothrombin3.4.21.50.611
1ypjUIBProthrombin3.4.21.50.608
1ta2176Prothrombin3.4.21.50.605
1d3dBZTProthrombin3.4.21.50.604
2v3oI26Prothrombin3.4.21.50.604
1bcuPRLProthrombin3.4.21.50.603
1c4uIH1Prothrombin3.4.21.50.599
1c5nESIProthrombin3.4.21.50.599
1ypeUIPProthrombin3.4.21.50.599
3qto10PProthrombin3.4.21.50.599
4banM6SProthrombin3.4.21.50.598
4baqM4ZProthrombin3.4.21.50.595
3p1799PProthrombin3.4.21.50.590
1mu6CDAProthrombin3.4.21.50.589
1vzqSHYProthrombin3.4.21.50.585
3c27DKKProthrombin3.4.21.50.584
1ghv120Prothrombin3.4.21.50.582
1ypmRA4Prothrombin3.4.21.50.581
1jwtBLIProthrombin3.4.21.50.580
4ayy9MXProthrombin3.4.21.50.578
1d9i00PProthrombin3.4.21.50.573
2uuk897Prothrombin3.4.21.50.571
4bahMELProthrombin3.4.21.50.568
2gdeSN3Prothrombin3.4.21.50.567
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.566
4n3l2FNProthrombin3.4.21.50.566
2cf9348Prothrombin3.4.21.50.561
2bdyUNBProthrombin3.4.21.50.560
1gj4132Prothrombin3.4.21.50.559
2uuj896Prothrombin3.4.21.50.558
2a2xNA9Prothrombin3.4.21.50.557
2pksG44Prothrombin3.4.21.50.556
1nzq162Prothrombin3.4.21.50.554
2v3hI25Prothrombin3.4.21.50.554
3qtv06PProthrombin3.4.21.50.554
1nm6L86Prothrombin3.4.21.50.552
4e7r0NWProthrombin3.4.21.50.550
4baoMVFProthrombin3.4.21.50.549
1d3pBT3Prothrombin3.4.21.50.548
1c4vIH2Prothrombin3.4.21.50.547
1gj5130Prothrombin3.4.21.50.546
1c4yIH3Prothrombin3.4.21.50.543
4loy6XSProthrombin3.4.21.50.543
2cf8ESHProthrombin3.4.21.50.536
4az29MUProthrombin3.4.21.50.536
2bxtC2DProthrombin3.4.21.50.533
1o5gCR9Prothrombin3.4.21.50.526
1o2g696Prothrombin3.4.21.50.523
1k22MELProthrombin3.4.21.50.521
1umaIN2Prothrombin3.4.21.50.521
2zhw12UProthrombin3.4.21.50.518
4rn615UProthrombin3.4.21.50.518
1w7gMIUProthrombin3.4.21.50.504
4ayv9MQProthrombin3.4.21.50.504
1c1uBAIProthrombin3.4.21.50.500
1riwOSCProthrombin3.4.21.50.499
4b1jA1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.499
1oytFSNProthrombin3.4.21.50.484
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.484
4fuf8UPUrokinase-type plasminogen activator3.4.21.730.480
2hxzH7JCathepsin S3.4.22.270.478
1wqvPSMCoagulation factor VII3.4.21.210.477
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.477
4fuj1U9Urokinase-type plasminogen activator3.4.21.730.474
4kgkGTPUncharacterized protein/0.474
2rqfJH3Hemolymph juvenile hormone binding protein/0.473
5cmx0G6Prothrombin3.4.21.50.473
2zp0PI0Coagulation factor VII3.4.21.210.469
4a802ANMajor pollen allergen Bet v 1-A/0.468
4fue7UPUrokinase-type plasminogen activator3.4.21.730.468
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.467
1rkwPNTHTH-type transcriptional regulator QacR/0.466
2nr4FMNConserved protein/0.466
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.465
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.463
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.463
1f20FADNitric oxide synthase, brain1.14.13.390.462
2e1mFADL-glutamate oxidase/0.462
2po7CHDFerrochelatase, mitochondrial4.99.1.10.462
2qimZEAClass 10 plant pathogenesis-related protein/0.461
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.461
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.461
1b2lNDCAlcohol dehydrogenase1.1.1.10.460
1oc1ASVIsopenicillin N synthase1.21.3.10.460
2abaSTRPentaerythritol tetranitrate reductase/0.460
2g8yNADHydroxycarboxylate dehydrogenase B/0.460
4dc1NDPPutative ketoacyl reductase1.3.10.460
4q71FADBifunctional protein PutA/0.459
1dr3TAPDihydrofolate reductase1.5.1.30.458
1pq944BOxysterols receptor LXR-beta/0.457
2rlcCHDCholoylglycine hydrolase3.5.1.240.457
2vyqFADFerredoxin--NADP reductase1.18.1.20.457
1vi2NADQuinate/shikimate dehydrogenase/0.456
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.456
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.456
2pg0FADAcyl-CoA dehydrogenase/0.456
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.456
4uthFMNXenobiotic reductase/0.456
1j1zATPArgininosuccinate synthase/0.455
1sl3170Prothrombin3.4.21.50.455
1tytFADTrypanothione reductase1.8.1.120.455
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.455
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.455
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.454
3c4hDRLPoly [ADP-ribose] polymerase 32.4.2.300.454
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.454
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3wqmB29Diterpene synthase3.1.7.80.454
4i4z2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.454
3vilSA0Beta-glucosidase/0.453
4d03NAPPhenylacetone monooxygenase1.14.13.920.453
4fuiUI3Urokinase-type plasminogen activator3.4.21.730.453
4kbyC2EStimulator of interferon genes protein/0.453
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.453
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.452
2ejzSAHDiphthine synthase/0.452
2zevIPEGeranylgeranyl pyrophosphate synthase/0.452
3pftFMNFlavin reductase/0.452
3vev0H4Glucokinase2.7.1.20.452
4lzwTHMUridine phosphorylase/0.452
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.451
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.451
2whqHI6Acetylcholinesterase3.1.1.70.451
4m0f1YKAcetylcholinesterase3.1.1.70.451
1pqc444Oxysterols receptor LXR-beta/0.450
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.450
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.450
3ai0PNWBeta-glucosidase/0.450
4c73TLH3-oxoacyl-ACP synthase/0.450
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.450
4yjdFADD-amino-acid oxidase1.4.3.30.450
2jk6FADTrypanothione reductase/0.449
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.449
2y5hY5HCoagulation factor X3.4.21.60.449
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3po6DT9Carbonic anhydrase 24.2.1.10.449
2aj4ANPGalactokinase2.7.1.60.448
2g1n1IGRenin3.4.23.150.448
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.448
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.448
3fp0FP015-O-acetyltransferase/0.448
3pm1ETHTH-type transcriptional regulator QacR/0.448
3swcSAHHistone-lysine N-methyltransferase EHMT1/0.448
4a87NARMajor pollen allergen Bet v 1-A/0.448
4fub4UPUrokinase-type plasminogen activator3.4.21.730.448
5jy1NADPutative short-chain dehydrogenase/reductase/0.448
1o9bNAIQuinate/shikimate dehydrogenase/0.447
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.447
4a8v2ANMajor pollen allergen Bet v 1-J/0.447
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.447
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2cndFADNitrate reductase [NADH]1.7.1.10.446
2g004QCCoagulation factor X3.4.21.60.446
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.446
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.446
3i7vB4PAP4A hydrolase/0.446
3mo0SAHHistone-lysine N-methyltransferase EHMT1/0.446
3zeiAWHO-acetylserine sulfhydrylase/0.446
2c4fGILCoagulation factor VII3.4.21.210.445
4xbfFADLysine-specific histone demethylase 1A10.445
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1fecFADTrypanothione reductase1.8.1.120.444
1nhkCMPNucleoside diphosphate kinase2.7.4.60.444
1tllFMNNitric oxide synthase, brain1.14.13.390.444
1tojHCIAspartate aminotransferase2.6.1.10.444
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.444
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.444
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.444
1npdNADQuinate/shikimate dehydrogenase/0.443
1owk303Urokinase-type plasminogen activator3.4.21.730.443
1q84TZ4Acetylcholinesterase3.1.1.70.443
2b9yFADPutative aminooxidase/0.443
2dxdANPNucleoside diphosphate kinase2.7.4.60.443
2gv8NDPThiol-specific monooxygenase1.14.130.443
4c72TLG3-oxoacyl-ACP synthase/0.443
4i1c1BEBeta-secretase 13.4.23.460.443
4m5pFMNNADPH dehydrogenase/0.443
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.442
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.442
2xuiTZ5Acetylcholinesterase3.1.1.70.442
3br3ETHTH-type transcriptional regulator QacR/0.442
3fhxPXLPyridoxal kinase2.7.1.350.442
3v4aPK1Androgen receptor/0.442
3zhoFMNNAD(P)H dehydrogenase (quinone)/0.442
1fmlRTLRetinol dehydratase/0.441
1oklMNSCarbonic anhydrase 24.2.1.10.441
1w34FADFerredoxin--NADP reductase1.18.1.20.441
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2fe4GDPRas-related protein Rab-6B/0.441
2iejS48Protein farnesyltransferase subunit beta2.5.1.580.441
2xugTZ4Acetylcholinesterase3.1.1.70.441
2zbaZBATrichothecene 3-O-acetyltransferase/0.441
4bekXK0Beta-secretase 13.4.23.460.441
4gtv7TRGeranylgeranyl transferase type-2 subunit beta2.5.1.600.441
4yfy0FXVioF/0.441
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.440
1kheGCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.440
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.440
2fznFADBifunctional protein PutA1.5.5.20.440
2v16C47Renin3.4.23.150.440
2x8hFADThioredoxin glutathione reductase/0.440
2ywlFADThioredoxin reductase related protein/0.440
3dufR1TPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.440
3dufR1TPyruvate dehydrogenase E1 component subunit beta1.2.4.10.440
3e8xNAPBH1520 protein/0.440
3otwCOAPhosphopantetheine adenylyltransferase/0.440
4g95OAGDihydrofolate reductase1.5.1.30.440
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.440
5cc9DDFDihydrofolate reductase1.5.1.30.440