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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
1mu8CDBProthrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1mu8CDBProthrombin3.4.21.51.000
1mu6CDAProthrombin3.4.21.50.775
1ta6177Prothrombin3.4.21.50.775
1zgv501Prothrombin3.4.21.50.725
1z71L17Prothrombin3.4.21.50.704
1zgi382Prothrombin3.4.21.50.680
1d6w00RProthrombin3.4.21.50.658
3c1kT15Prothrombin3.4.21.50.655
3qwc98PProthrombin3.4.21.50.649
1t4v14AProthrombin3.4.21.50.648
2jh6894Prothrombin3.4.21.50.645
2zfq45UProthrombin3.4.21.50.643
1mueCDDProthrombin3.4.21.50.639
2bvs2CEProthrombin3.4.21.50.639
1t4u81AProthrombin3.4.21.50.637
2zc922UProthrombin3.4.21.50.637
2jh5895Prothrombin3.4.21.50.634
2jh0701Prothrombin3.4.21.50.633
2gdeSN3Prothrombin3.4.21.50.631
1ypeUIPProthrombin3.4.21.50.626
2ziq26UProthrombin3.4.21.50.626
1yplRA8Prothrombin3.4.21.50.625
2zi224UProthrombin3.4.21.50.624
2zda32UProthrombin3.4.21.50.621
2cn0F25Prothrombin3.4.21.50.614
1nm6L86Prothrombin3.4.21.50.611
1ypgUIRProthrombin3.4.21.50.610
2a2xNA9Prothrombin3.4.21.50.608
1d4pBPPProthrombin3.4.21.50.606
2r2mI50Prothrombin3.4.21.50.603
2zhf49UProthrombin3.4.21.50.601
3dhk23UProthrombin3.4.21.50.600
2uuk897Prothrombin3.4.21.50.599
1c4vIH2Prothrombin3.4.21.50.598
1c4yIH3Prothrombin3.4.21.50.598
2zfr46UProthrombin3.4.21.50.594
2zhq27UProthrombin3.4.21.50.594
4ax9N5NProthrombin3.4.21.50.594
2cf8ESHProthrombin3.4.21.50.593
2zdv37UProthrombin3.4.21.50.593
3egkM18Prothrombin3.4.21.50.592
2anmCDOProthrombin3.4.21.50.589
1nzq162Prothrombin3.4.21.50.588
1ta2176Prothrombin3.4.21.50.588
4lxb7R9Prothrombin3.4.21.50.587
2zhe13UProthrombin3.4.21.50.586
1d3dBZTProthrombin3.4.21.50.585
1ypmRA4Prothrombin3.4.21.50.583
2zgx29UProthrombin3.4.21.50.583
1xm1GAHProthrombin3.4.21.50.581
1d9i00PProthrombin3.4.21.50.578
2cf9348Prothrombin3.4.21.50.578
4ayy9MXProthrombin3.4.21.50.577
2znk31UProthrombin3.4.21.50.576
1ghv120Prothrombin3.4.21.50.575
1gj4132Prothrombin3.4.21.50.575
1d3pBT3Prothrombin3.4.21.50.573
2zg050UProthrombin3.4.21.50.573
3biv11UProthrombin3.4.21.50.573
1a4wQWEProthrombin3.4.21.50.569
2v3oI26Prothrombin3.4.21.50.569
1o2g696Prothrombin3.4.21.50.568
4az29MUProthrombin3.4.21.50.568
4hfp15UProthrombin3.4.21.50.568
1afeALZProthrombin3.4.21.50.565
1bcuPRLProthrombin3.4.21.50.565
4ayv9MQProthrombin3.4.21.50.565
2bdyUNBProthrombin3.4.21.50.564
1o5gCR9Prothrombin3.4.21.50.563
4n3l2FNProthrombin3.4.21.50.562
1sb1165Prothrombin3.4.21.50.561
1ae8AZLProthrombin3.4.21.50.559
2zfp19UProthrombin3.4.21.50.556
1riwOSCProthrombin3.4.21.50.555
1uvsI11Prothrombin3.4.21.50.553
1k21IGNProthrombin3.4.21.50.552
1oytFSNProthrombin3.4.21.50.551
1gj5130Prothrombin3.4.21.50.550
1ypjUIBProthrombin3.4.21.50.550
4e7r0NWProthrombin3.4.21.50.549
1c5nESIProthrombin3.4.21.50.546
1ktsC24Prothrombin3.4.21.50.543
4loy6XSProthrombin3.4.21.50.543
1c4uIH1Prothrombin3.4.21.50.542
2v3hI25Prothrombin3.4.21.50.542
2zff53UProthrombin3.4.21.50.542
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.541
3biu10UProthrombin3.4.21.50.540
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.536
2zhw12UProthrombin3.4.21.50.534
1k22MELProthrombin3.4.21.50.531
3eq02TSProthrombin3.4.21.50.531
1ypkCCRProthrombin3.4.21.50.530
2zf051UProthrombin3.4.21.50.530
1o0d163Prothrombin3.4.21.50.529
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.526
3dux64UProthrombin3.4.21.50.526
4bamMM9Prothrombin3.4.21.50.526
3f6891UProthrombin3.4.21.50.523
2zgb21UProthrombin3.4.21.50.519
3qto10PProthrombin3.4.21.50.518
1nt1T76Prothrombin3.4.21.50.512
1jwtBLIProthrombin3.4.21.50.511
3qtv06PProthrombin3.4.21.50.511
3p1799PProthrombin3.4.21.50.510
2pksG44Prothrombin3.4.21.50.507
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.506
1vzqSHYProthrombin3.4.21.50.503
4m6jNDPDihydrofolate reductase1.5.1.30.503
4bakM67Prothrombin3.4.21.50.500
4rn615UProthrombin3.4.21.50.498
1zrb062Prothrombin3.4.21.50.494
3zoiM2WIsopenicillin N synthase1.21.3.10.490
1zsk421Coagulation factor XI3.4.21.270.489
1dr5NAPDihydrofolate reductase1.5.1.30.487
1dr2TAPDihydrofolate reductase1.5.1.30.485
4bfxZVXPantothenate kinase2.7.1.330.484
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.482
2rqfJH3Hemolymph juvenile hormone binding protein/0.481
2uuj896Prothrombin3.4.21.50.478
2zcvNDPQuinone oxidoreductase 21.6.5.20.478
4bahMELProthrombin3.4.21.50.478
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.477
1owe675Urokinase-type plasminogen activator3.4.21.730.477
5cmx0G6Prothrombin3.4.21.50.477
4a862ANMajor pollen allergen Bet v 1-A/0.476
1hb3SCVIsopenicillin N synthase1.21.3.10.475
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.473
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.473
4fuf8UPUrokinase-type plasminogen activator3.4.21.730.473
1ia4TQ6Dihydrofolate reductase1.5.1.30.472
2j4lUTPUridylate kinase2.7.4.220.472
3c27DKKProthrombin3.4.21.50.472
4q71FADBifunctional protein PutA/0.472
4bttVYRCoagulation factor X3.4.21.60.471
3oafOAGDihydrofolate reductase1.5.1.30.470
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.469
4g95OAGDihydrofolate reductase1.5.1.30.469
4kbyC2EStimulator of interferon genes protein/0.469
1bk0ACVIsopenicillin N synthase1.21.3.10.468
1qiqACCIsopenicillin N synthase1.21.3.10.468
2g21L1BRenin3.4.23.150.468
2qimZEAClass 10 plant pathogenesis-related protein/0.468
1c1wBAHProthrombin3.4.21.50.467
2bxtC2DProthrombin3.4.21.50.467
2cv2GSUGlutamate--tRNA ligase6.1.1.170.467
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.467
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.467
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.466
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.466
2y6fM9FIsopenicillin N synthase1.21.3.10.466
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.466
3utu1TSProthrombin3.4.21.50.465
1drhNAPDihydrofolate reductase1.5.1.30.463
3d84NDPDihydrofolate reductase1.5.1.30.463
3qe2FMNNADPH--cytochrome P450 reductase/0.463
3sorO58Coagulation factor XI3.4.21.270.463
4i1c1BEBeta-secretase 13.4.23.460.463
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.462
2jb4A14Isopenicillin N synthase1.21.3.10.462
4xguADPPutative pachytene checkpoint protein 2/0.462
1bil0IURenin3.4.23.150.461
1hb1OCVIsopenicillin N synthase1.21.3.10.461
4fuiUI3Urokinase-type plasminogen activator3.4.21.730.461
2nr4FMNConserved protein/0.460
4ey6GNTAcetylcholinesterase3.1.1.70.460
2g1s4IGRenin3.4.23.150.459
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.459
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.459
1wqvPSMCoagulation factor VII3.4.21.210.458
2g1y5IGRenin3.4.23.150.458
1ia3TQ5Dihydrofolate reductase1.5.1.30.457
1w7gMIUProthrombin3.4.21.50.457
3d91REMRenin3.4.23.150.457
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.457
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.457
4a83DXCMajor pollen allergen Bet v 1-A/0.457
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.457
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.457
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.456
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.456
2xfyACXBeta-amylase3.2.1.20.456
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3v0xANHCationic trypsin3.4.21.40.456
2g247IGRenin3.4.23.150.455
2iviACWIsopenicillin N synthase1.21.3.10.455
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.455
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.455
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.455
2b36NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.454
3hl0NADMaleylacetate reductase/0.454
3k1wBFXRenin3.4.23.150.454
4j0v1H7Beta-secretase 13.4.23.460.454
1dr3TAPDihydrofolate reductase1.5.1.30.453
1ex75GPGuanylate kinase2.7.4.80.453
1nj6A5AProline--tRNA ligase/0.453
1rneC60Renin3.4.23.150.453
1umkFADNADH-cytochrome b5 reductase 31.6.2.20.453
3s1dZIRCytokinin dehydrogenase 11.5.99.120.453
4a802ANMajor pollen allergen Bet v 1-A/0.453
4azy7F3Beta-secretase 13.4.23.460.453
1blzACVIsopenicillin N synthase1.21.3.10.452
1nfyRTRCoagulation factor X3.4.21.60.452
1u1gBBBUridine phosphorylase2.4.2.30.452
2g1o2IGRenin3.4.23.150.452
2r59PH0Leukotriene A-4 hydrolase3.3.2.60.452
2vbdV10Isopenicillin N synthase1.21.3.10.452
4banM6SProthrombin3.4.21.50.452
1obnASVIsopenicillin N synthase1.21.3.10.451
1xe65FPPlasmepsin-23.4.23.390.451
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.451
2g20L1ARenin3.4.23.150.451
2y60M8FIsopenicillin N synthase1.21.3.10.451
3g70A5TRenin3.4.23.150.451
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
3kxw1ZZSaframycin Mx1 synthetase B/0.451
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.451
3zksWZVBeta-secretase 23.4.23.450.451
4acuQN7Beta-secretase 13.4.23.460.451
2fzmFADBifunctional protein PutA1.5.5.20.450
2g1n1IGRenin3.4.23.150.450
3oadLPORenin3.4.23.150.450
3qj0QI3Botulinum neurotoxin type A3.4.24.690.450
4b67NAPL-ornithine N(5)-monooxygenase/0.450
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.450
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.450
4rvgTYDD-mycarose 3-C-methyltransferase/0.450
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.450
1dr3HBIDihydrofolate reductase1.5.1.30.449
1iqgXMECoagulation factor X3.4.21.60.449
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.449
3dg8NDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.449
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.449
3h3t16HCollagen type IV alpha-3-binding protein/0.449
3phiNDPShikimate dehydrogenase (NADP(+))/0.449
3qlrNDPDihydrofolate reductase1.5.1.30.449
4a81DXCMajor pollen allergen Bet v 1-A/0.449
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.449
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.449
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.449
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.448
1oc1ASVIsopenicillin N synthase1.21.3.10.448
1sqtUI3Urokinase-type plasminogen activator3.4.21.730.448
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
2dhfDZFDihydrofolate reductase1.5.1.30.448
2i4qUA4Renin3.4.23.150.448
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.448
3bnkFMNFlavoredoxin/0.448
3vyfVYFRenin3.4.23.150.448
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4cdmFO1Deoxyribodipyrimidine photolyase/0.448
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.448
5fd8A5APutative carboxypeptidase yocD/0.448
5la6GDPTubulin beta-2B chain/0.448
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.447
1esmCOAPantothenate kinase2.7.1.330.447
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.447
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.447
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.447
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
2hxzH7JCathepsin S3.4.22.270.447
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.447
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3fpdSAHHistone-lysine N-methyltransferase EHMT1/0.447
3oqfS51Renin3.4.23.150.447
3qt62P0Mevalonate diphosphate decarboxylase/0.447
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.447
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.447
4e2yJHZMethyltransferase/0.447
4jlm1NNDeoxycytidine kinase2.7.1.740.447
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.447
4xr9NADCalS8/0.447
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.446
1uk1FRQPoly [ADP-ribose] polymerase 12.4.2.300.446
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2a5kAZPReplicase polyprotein 1ab3.4.220.446
2cjiGSKCoagulation factor X3.4.21.60.446
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.446
3fr5I4AFatty acid-binding protein, adipocyte/0.446
3k8q22APurine nucleoside phosphorylase2.4.2.10.446
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.446
4b1e6T6Beta-secretase 13.4.23.460.446
4esoNAPPutative oxidoreductase/0.446
4fue7UPUrokinase-type plasminogen activator3.4.21.730.446
1lceTMFThymidylate synthase/0.445
2w3bNDPDihydrofolate reductase1.5.1.30.445
2ylrFADPhenylacetone monooxygenase1.14.13.920.445
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3hiiPNTAmiloride-sensitive amine oxidase [copper-containing]/0.445
3pftFMNFlavin reductase/0.445
4p9dTMPDeoxycytidylate deaminase/0.445
1cneFADNitrate reductase [NADH]1.7.1.10.444
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1pqc444Oxysterols receptor LXR-beta/0.444
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.444
1uh5TCLEnoyl-ACP reductase/0.444
2b58COADiamine acetyltransferase 1/0.444
2dvlFADAcyl-CoA dehydrogenase/0.444
2fznFADBifunctional protein PutA1.5.5.20.444
2iko7IGRenin3.4.23.150.444
2il2LIXRenin3.4.23.150.444
2y5hY5HCoagulation factor X3.4.21.60.444
3h3r14HCollagen type IV alpha-3-binding protein/0.444
4baqM4ZProthrombin3.4.21.50.444
4fm80UQBeta-secretase 13.4.23.460.444
4o1mNADEnoyl-acyl carrier reductase/0.444
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.444
5dsyUHBPoly [ADP-ribose] polymerase 22.4.2.300.444
1cnfFADNitrate reductase [NADH]1.7.1.10.443
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1m78NDPDihydrofolate reductase1.5.1.30.443
1p4aPCPPur operon repressor/0.443
1rszDIHPurine nucleoside phosphorylase2.4.2.10.443
1u71MXADihydrofolate reductase1.5.1.30.443
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.443
2bu9HFVIsopenicillin N synthase1.21.3.10.443
2ym1FADPhenylacetone monooxygenase1.14.13.920.443
3fvqATPFe(3+) ions import ATP-binding protein FbpC/0.443
3nxxNDPDihydrofolate reductase1.5.1.30.443
3zg6APRNAD-dependent protein deacetylase sirtuin-63.5.10.443
4bftZVTPantothenate kinase2.7.1.330.443
4fud6UPUrokinase-type plasminogen activator3.4.21.730.443
4tx9AMZPhosphoribosyl isomerase A/0.443
1dhfFOLDihydrofolate reductase1.5.1.30.442
1k7fIAVTryptophan synthase alpha chain/0.442
1udaUFGUDP-glucose 4-epimerase5.1.3.20.442
1zdwFLVPrenyltransferase/0.442
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.442
2g1r3IGRenin3.4.23.150.442
2vyqFADFerredoxin--NADP reductase1.18.1.20.442
3bk2U5PRibonuclease J/0.442
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4fub4UPUrokinase-type plasminogen activator3.4.21.730.442
4h1e10JBeta-secretase 13.4.23.460.442
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.442
1f92UKPUrokinase-type plasminogen activator3.4.21.730.441
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
2b9yFADPutative aminooxidase/0.441
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.441
4bfsZVSPantothenate kinase2.7.1.330.441
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.440
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.440
2q0lNAPThioredoxin reductase1.8.1.90.440
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.440
2vivVG2Urokinase-type plasminogen activator3.4.21.730.440
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.440
3ogwIMNLactoperoxidase1.11.1.70.440
3p0fBAUUridine phosphorylase 22.4.2.30.440
4bfvZVVPantothenate kinase2.7.1.330.440
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
4ead0NPThymidine phosphorylase2.4.2.40.440
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4jjiNADAlcohol dehydrogenase class-3/0.440
4r20AERCytochrome P450 family 17 polypeptide 2/0.440
5ilwURIRibosome inactivating protein/0.440
5irnADPNucleotide binding oligomerization domain containing 2/0.440