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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
1o2g696Prothrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1o2g696Prothrombin3.4.21.51.000
1gj5130Prothrombin3.4.21.50.902
1o5gCR9Prothrombin3.4.21.50.675
1gj4132Prothrombin3.4.21.50.639
4hfp15UProthrombin3.4.21.50.577
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.570
1c4vIH2Prothrombin3.4.21.50.567
2v3oI26Prothrombin3.4.21.50.550
4e7r0NWProthrombin3.4.21.50.548
1oytFSNProthrombin3.4.21.50.544
1d3pBT3Prothrombin3.4.21.50.543
1c4uIH1Prothrombin3.4.21.50.540
2cf8ESHProthrombin3.4.21.50.540
4lxb7R9Prothrombin3.4.21.50.536
1ypjUIBProthrombin3.4.21.50.535
1xm1GAHProthrombin3.4.21.50.534
2cf9348Prothrombin3.4.21.50.534
1zsk421Coagulation factor XI3.4.21.270.532
1ghv120Prothrombin3.4.21.50.530
1ypgUIRProthrombin3.4.21.50.530
5cmx0G6Prothrombin3.4.21.50.528
1nm6L86Prothrombin3.4.21.50.524
1ypeUIPProthrombin3.4.21.50.524
4ayv9MQProthrombin3.4.21.50.524
2jh6894Prothrombin3.4.21.50.521
2bvs2CEProthrombin3.4.21.50.519
2cn0F25Prothrombin3.4.21.50.513
1ypmRA4Prothrombin3.4.21.50.512
4ayy9MXProthrombin3.4.21.50.507
4loy6XSProthrombin3.4.21.50.506
2zhf49UProthrombin3.4.21.50.502
4fue7UPUrokinase-type plasminogen activator3.4.21.730.502
2jh0701Prothrombin3.4.21.50.499
2a2xNA9Prothrombin3.4.21.50.496
1mu8CDBProthrombin3.4.21.50.493
3egkM18Prothrombin3.4.21.50.493
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.488
4rn615UProthrombin3.4.21.50.484
2vivVG2Urokinase-type plasminogen activator3.4.21.730.481
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.480
1w7gMIUProthrombin3.4.21.50.479
3dhk23UProthrombin3.4.21.50.476
1c5nESIProthrombin3.4.21.50.474
2uuk897Prothrombin3.4.21.50.473
5dp2NAPCurF/0.470
1bcuPRLProthrombin3.4.21.50.468
1riwOSCProthrombin3.4.21.50.467
1sb1165Prothrombin3.4.21.50.467
1fm4DXCMajor pollen allergen Bet v 1-L/0.466
2x7hPFNProstaglandin reductase 310.466
2gdeSN3Prothrombin3.4.21.50.465
3phiNDPShikimate dehydrogenase (NADP(+))/0.463
1blzACVIsopenicillin N synthase1.21.3.10.460
1uvsI11Prothrombin3.4.21.50.460
2ifaFMNUncharacterized protein/0.460
4a83DXCMajor pollen allergen Bet v 1-A/0.460
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.459
1qiqACCIsopenicillin N synthase1.21.3.10.458
4kbyC2EStimulator of interferon genes protein/0.457
2jb4A14Isopenicillin N synthase1.21.3.10.456
2vbdV10Isopenicillin N synthase1.21.3.10.456
1bim0QBRenin3.4.23.150.455
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.455
1zdwFLVPrenyltransferase/0.455
3junAKDPhenazine biosynthesis protein A/B/0.455
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.455
1bk0ACVIsopenicillin N synthase1.21.3.10.454
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1o0d163Prothrombin3.4.21.50.452
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.451
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.451
4az29MUProthrombin3.4.21.50.450
1hb3SCVIsopenicillin N synthase1.21.3.10.449
1xddAAYIntegrin alpha-L/0.449
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.449
3vswR31Renin3.4.23.150.448
3zoiM2WIsopenicillin N synthase1.21.3.10.448
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.447
1obnASVIsopenicillin N synthase1.21.3.10.446
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3nsh957Beta-secretase 13.4.23.460.446
4i0i957Beta-secretase 13.4.23.460.446
2g226IGRenin3.4.23.150.445
3duyAFJBeta-secretase 13.4.23.460.445
4a84DXCMajor pollen allergen Bet v 1-A/0.445
4g3jVNTLanosterol 14-alpha-demethylase/0.445
4j7hTRHPCZA361.3/0.445
2g1n1IGRenin3.4.23.150.444
2hizLIJBeta-secretase 13.4.23.460.444
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.444
3d91REMRenin3.4.23.150.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3hl0NADMaleylacetate reductase/0.444
3ig6438Urokinase-type plasminogen activator3.4.21.730.444
4rvgTYDD-mycarose 3-C-methyltransferase/0.444
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4j7gTRHPCZA361.3/0.443
3k5c0BIBeta-secretase 13.4.23.460.442
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4y0kNAPAntE/0.442
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
2ejzSAHDiphthine synthase/0.441
3tfyCOAN-alpha-acetyltransferase 502.3.10.441
3zkyWT4Isopenicillin N synthase1.21.3.10.441
4bfsZVSPantothenate kinase2.7.1.330.441
2ziq26UProthrombin3.4.21.50.440
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.440
4b65FADL-ornithine N(5)-monooxygenase/0.440
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.440