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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
2a2xNA9Prothrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2a2xNA9Prothrombin3.4.21.51.000
1yplRA8Prothrombin3.4.21.50.697
1ypgUIRProthrombin3.4.21.50.674
1nm6L86Prothrombin3.4.21.50.661
1z71L17Prothrombin3.4.21.50.650
1xm1GAHProthrombin3.4.21.50.643
1gj4132Prothrombin3.4.21.50.636
1d6w00RProthrombin3.4.21.50.633
3c1kT15Prothrombin3.4.21.50.632
1ta6177Prothrombin3.4.21.50.628
1d3pBT3Prothrombin3.4.21.50.625
1t4v14AProthrombin3.4.21.50.623
1d3dBZTProthrombin3.4.21.50.622
1ypmRA4Prothrombin3.4.21.50.622
2cn0F25Prothrombin3.4.21.50.622
2cf9348Prothrombin3.4.21.50.614
2zfq45UProthrombin3.4.21.50.614
3qwc98PProthrombin3.4.21.50.609
1sb1165Prothrombin3.4.21.50.607
2zi224UProthrombin3.4.21.50.607
2uuk897Prothrombin3.4.21.50.605
4ayy9MXProthrombin3.4.21.50.605
2ziq26UProthrombin3.4.21.50.602
1mu8CDBProthrombin3.4.21.50.601
2cf8ESHProthrombin3.4.21.50.598
2zc922UProthrombin3.4.21.50.594
2gdeSN3Prothrombin3.4.21.50.593
3dhk23UProthrombin3.4.21.50.592
1d4pBPPProthrombin3.4.21.50.590
2jh5895Prothrombin3.4.21.50.589
1zgi382Prothrombin3.4.21.50.588
4ax9N5NProthrombin3.4.21.50.588
1c4vIH2Prothrombin3.4.21.50.587
1bcuPRLProthrombin3.4.21.50.586
4lxb7R9Prothrombin3.4.21.50.585
2anmCDOProthrombin3.4.21.50.583
3egkM18Prothrombin3.4.21.50.581
1ypjUIBProthrombin3.4.21.50.580
1mu6CDAProthrombin3.4.21.50.579
2bvs2CEProthrombin3.4.21.50.579
1ypeUIPProthrombin3.4.21.50.578
1t4u81AProthrombin3.4.21.50.577
1k22MELProthrombin3.4.21.50.572
2zhq27UProthrombin3.4.21.50.572
1o0d163Prothrombin3.4.21.50.571
2zhe13UProthrombin3.4.21.50.571
2bdyUNBProthrombin3.4.21.50.569
1gj5130Prothrombin3.4.21.50.568
1ypkCCRProthrombin3.4.21.50.568
1mueCDDProthrombin3.4.21.50.566
4hfp15UProthrombin3.4.21.50.564
2jh0701Prothrombin3.4.21.50.563
1ktsC24Prothrombin3.4.21.50.562
1d9i00PProthrombin3.4.21.50.561
2zda32UProthrombin3.4.21.50.561
2znk31UProthrombin3.4.21.50.557
1ghv120Prothrombin3.4.21.50.556
1o2g696Prothrombin3.4.21.50.556
2r2mI50Prothrombin3.4.21.50.556
1zgv501Prothrombin3.4.21.50.555
4n3l2FNProthrombin3.4.21.50.555
2zhf49UProthrombin3.4.21.50.554
4ayv9MQProthrombin3.4.21.50.554
2jh6894Prothrombin3.4.21.50.551
3biv11UProthrombin3.4.21.50.551
1o5gCR9Prothrombin3.4.21.50.550
1nzq162Prothrombin3.4.21.50.548
1zrb062Prothrombin3.4.21.50.546
2v3hI25Prothrombin3.4.21.50.544
2zdv37UProthrombin3.4.21.50.540
1ta2176Prothrombin3.4.21.50.538
2zfr46UProthrombin3.4.21.50.538
1uvsI11Prothrombin3.4.21.50.535
2zhw12UProthrombin3.4.21.50.534
1ae8AZLProthrombin3.4.21.50.532
1c4uIH1Prothrombin3.4.21.50.532
1a4wQWEProthrombin3.4.21.50.528
1c4yIH3Prothrombin3.4.21.50.528
1afeALZProthrombin3.4.21.50.526
2zgx29UProthrombin3.4.21.50.525
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.525
4rn615UProthrombin3.4.21.50.522
1k21IGNProthrombin3.4.21.50.521
1c5nESIProthrombin3.4.21.50.520
1riwOSCProthrombin3.4.21.50.520
2v3oI26Prothrombin3.4.21.50.513
3biu10UProthrombin3.4.21.50.512
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.511
4e7r0NWProthrombin3.4.21.50.511
4az29MUProthrombin3.4.21.50.510
4loy6XSProthrombin3.4.21.50.510
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.509
2zff53UProthrombin3.4.21.50.508
3f6891UProthrombin3.4.21.50.504
4g95OAGDihydrofolate reductase1.5.1.30.504
2zf051UProthrombin3.4.21.50.501
2zg050UProthrombin3.4.21.50.501
3eq02TSProthrombin3.4.21.50.498
2pksG44Prothrombin3.4.21.50.497
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.493
1zsk421Coagulation factor XI3.4.21.270.492
3dux64UProthrombin3.4.21.50.489
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.488
2zfp19UProthrombin3.4.21.50.487
3ctyFADProbable thioredoxin reductase/0.487
1iqgXMECoagulation factor X3.4.21.60.484
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.482
2qimZEAClass 10 plant pathogenesis-related protein/0.480
2uuj896Prothrombin3.4.21.50.480
3p1799PProthrombin3.4.21.50.480
3v2uATPProtein GAL3/0.480
3qto10PProthrombin3.4.21.50.479
3v0xANHCationic trypsin3.4.21.40.477
2zgb21UProthrombin3.4.21.50.476
3oqfS51Renin3.4.23.150.476
1jwtBLIProthrombin3.4.21.50.474
1gky5GPGuanylate kinase2.7.4.80.473
1vzqSHYProthrombin3.4.21.50.473
3adaNADSubunit alpha of sarocosine oxidase/0.473
4bupSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.473
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.473
2rqfJH3Hemolymph juvenile hormone binding protein/0.472
1bil0IURenin3.4.23.150.471
2g1o2IGRenin3.4.23.150.470
2w3bNDPDihydrofolate reductase1.5.1.30.470
1ex75GPGuanylate kinase2.7.4.80.469
1w7gMIUProthrombin3.4.21.50.469
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.469
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.469
4jlk1NODeoxycytidine kinase2.7.1.740.469
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.468
1dr3TAPDihydrofolate reductase1.5.1.30.467
2g1n1IGRenin3.4.23.150.467
3oqkS52Renin3.4.23.150.467
3phiNDPShikimate dehydrogenase (NADP(+))/0.467
3qtv06PProthrombin3.4.21.50.467
4bakM67Prothrombin3.4.21.50.467
4baoMVFProthrombin3.4.21.50.467
1rneC60Renin3.4.23.150.466
4btu6XSCoagulation factor X3.4.21.60.466
1vja7INUrokinase-type plasminogen activator3.4.21.730.465
1sqtUI3Urokinase-type plasminogen activator3.4.21.730.464
1sl3170Prothrombin3.4.21.50.463
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.463
3oafOAGDihydrofolate reductase1.5.1.30.463
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.463
4xguADPPutative pachytene checkpoint protein 2/0.463
5cmx0G6Prothrombin3.4.21.50.463
1drhNAPDihydrofolate reductase1.5.1.30.461
1xvtCOAL-carnitine CoA-transferase/0.461
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1pq944BOxysterols receptor LXR-beta/0.460
1qiqACCIsopenicillin N synthase1.21.3.10.460
3qt62P0Mevalonate diphosphate decarboxylase/0.460
2hk9NAPShikimate dehydrogenase (NADP(+))/0.459
1u1gBBBUridine phosphorylase2.4.2.30.458
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.457
2dhfDZFDihydrofolate reductase1.5.1.30.457
2nr4FMNConserved protein/0.457
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.457
3fr5I4AFatty acid-binding protein, adipocyte/0.457
3nmpPYVAbscisic acid receptor PYL2/0.457
3own3OXRenin3.4.23.150.457
1b2lNDCAlcohol dehydrogenase1.1.1.10.456
1bim0QBRenin3.4.23.150.456
1vf3GDNGlutathione S-transferase 32.5.1.180.456
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
3k1wBFXRenin3.4.23.150.456
4esoNAPPutative oxidoreductase/0.456
4fuiUI3Urokinase-type plasminogen activator3.4.21.730.456
1nfyRTRCoagulation factor X3.4.21.60.454
1owe675Urokinase-type plasminogen activator3.4.21.730.454
2g1r3IGRenin3.4.23.150.454
2iko7IGRenin3.4.23.150.454
2ikuLIYRenin3.4.23.150.454
2vqzMGTPolymerase basic protein 2/0.454
4jlm1NNDeoxycytidine kinase2.7.1.740.454
4mlp2CXCryptochrome-2/0.454
1obnASVIsopenicillin N synthase1.21.3.10.453
3aosJH2Hemolymph juvenile hormone binding protein/0.453
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.452
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.452
1rszDIHPurine nucleoside phosphorylase2.4.2.10.452
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3vswR31Renin3.4.23.150.452
1toiHCIAspartate aminotransferase2.6.1.10.451
2g1y5IGRenin3.4.23.150.451
2wd8VGFPteridine reductase/0.451
3c27DKKProthrombin3.4.21.50.451
3h3sH15Collagen type IV alpha-3-binding protein/0.451
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.450
3h3qH13Collagen type IV alpha-3-binding protein/0.450
3hwxTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.450
4l7h1W1Beta-secretase 13.4.23.460.450
1qoqIGPTryptophan synthase alpha chain/0.449
2g004QCCoagulation factor X3.4.21.60.449
2imlFMNUncharacterized protein/0.449
2jt2C90UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.449
2v13C40Renin3.4.23.150.449
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3zv7NHGAcetylcholinesterase3.1.1.70.449
1ma0NADAlcohol dehydrogenase class-31.1.1.10.448
1nt1T76Prothrombin3.4.21.50.448
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.448
2g247IGRenin3.4.23.150.448
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.448
2qbuSAHPrecorrin-2 methyltransferase/0.448
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
4ead0NPThymidine phosphorylase2.4.2.40.448
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.448
4nwzFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.448
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.447
2g21L1BRenin3.4.23.150.447
2v16C47Renin3.4.23.150.447
2xukTZ5Acetylcholinesterase3.1.1.70.447
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4fub4UPUrokinase-type plasminogen activator3.4.21.730.447
1dr5NAPDihydrofolate reductase1.5.1.30.446
1iqeXMBCoagulation factor X3.4.21.60.446
1lv89PPPurine nucleoside phosphorylase2.4.2.10.446
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.446
2il2LIXRenin3.4.23.150.446
2y5gFJDCoagulation factor X3.4.21.60.446
3vsxR32Renin3.4.23.150.446
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.446
2abaSTRPentaerythritol tetranitrate reductase/0.445
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2cndFADNitrate reductase [NADH]1.7.1.10.445
1cjkFOKAdenylate cyclase type 2/0.444
1cjkFOKAdenylate cyclase type 5/0.444
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
2cekN8TAcetylcholinesterase3.1.1.70.444
2e94364Geranylgeranyl pyrophosphate synthase/0.444
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.444
2vivVG2Urokinase-type plasminogen activator3.4.21.730.444
2x3jATPAcsD/0.444
2xvv9DNSerum albumin/0.444
3own3OWRenin3.4.23.150.444
4fuf8UPUrokinase-type plasminogen activator3.4.21.730.444
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.444
1dr2TAPDihydrofolate reductase1.5.1.30.443
1gsfEAAGlutathione S-transferase A12.5.1.180.443
1hb3SCVIsopenicillin N synthase1.21.3.10.443
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.443
2g1s4IGRenin3.4.23.150.443
2geuCOKPantothenate kinase2.7.1.330.443
3af1GDPPantothenate kinase2.7.1.330.443
3d84NDPDihydrofolate reductase1.5.1.30.443
3djfBC3Purine nucleoside phosphorylase/0.443
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.443
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.443
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.443
3oadLPORenin3.4.23.150.443
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.443
4jlj1NMDeoxycytidine kinase2.7.1.740.443
1lvu9PPPurine nucleoside phosphorylase2.4.2.10.442
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.442
2viyVG3Beta-secretase 13.4.23.460.442
2xviFADPutative flavin-containing monooxygenase/0.442
3g70A5TRenin3.4.23.150.442
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.442
5a0112VO-glycosyltransferase/0.442
1bwlFMNNADPH dehydrogenase 11.6.99.10.441
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.441
1rx1NAPDihydrofolate reductase1.5.1.30.441
1ygjRMCPyridoxal kinase2.7.1.350.441
2i4qUA4Renin3.4.23.150.441
2xuhTZ4Acetylcholinesterase3.1.1.70.441
4brdANPEctonucleoside triphosphate diphosphohydrolase I/0.441
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.441
4m6jNDPDihydrofolate reductase1.5.1.30.441
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.441
5fmmMGTPolymerase basic protein 2/0.441
1pd9CO4Dihydrofolate reductase1.5.1.30.440
1sq5ADPPantothenate kinase2.7.1.330.440
1uk1FRQPoly [ADP-ribose] polymerase 12.4.2.300.440
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.440
2xugTZ4Acetylcholinesterase3.1.1.70.440
3hiiPNTAmiloride-sensitive amine oxidase [copper-containing]/0.440
3zkpERBErythromycin C-12 hydroxylase1.14.13.1540.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440