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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
2pksG44Prothrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2pksG44Prothrombin3.4.21.51.000
2bdyUNBProthrombin3.4.21.50.689
1ypmRA4Prothrombin3.4.21.50.667
1d6w00RProthrombin3.4.21.50.665
2zhq27UProthrombin3.4.21.50.661
2zgx29UProthrombin3.4.21.50.644
4ax9N5NProthrombin3.4.21.50.644
1jwtBLIProthrombin3.4.21.50.639
2v3oI26Prothrombin3.4.21.50.639
1ypjUIBProthrombin3.4.21.50.636
2r2mI50Prothrombin3.4.21.50.636
2zda32UProthrombin3.4.21.50.635
2zgb21UProthrombin3.4.21.50.632
2zhw12UProthrombin3.4.21.50.631
2anmCDOProthrombin3.4.21.50.630
2zc922UProthrombin3.4.21.50.626
1zgv501Prothrombin3.4.21.50.624
2zfr46UProthrombin3.4.21.50.624
2zi224UProthrombin3.4.21.50.624
1mu6CDAProthrombin3.4.21.50.621
2zfp19UProthrombin3.4.21.50.621
1ypeUIPProthrombin3.4.21.50.620
1ypgUIRProthrombin3.4.21.50.617
1d9i00PProthrombin3.4.21.50.616
1nm6L86Prothrombin3.4.21.50.616
2zhf49UProthrombin3.4.21.50.616
4bahMELProthrombin3.4.21.50.614
2zf051UProthrombin3.4.21.50.612
1nzq162Prothrombin3.4.21.50.611
2zfq45UProthrombin3.4.21.50.609
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.609
1d4pBPPProthrombin3.4.21.50.608
3eq02TSProthrombin3.4.21.50.608
4n3l2FNProthrombin3.4.21.50.607
1d3dBZTProthrombin3.4.21.50.606
2v3hI25Prothrombin3.4.21.50.606
3p1799PProthrombin3.4.21.50.605
1xm1GAHProthrombin3.4.21.50.603
2znk31UProthrombin3.4.21.50.603
1c4uIH1Prothrombin3.4.21.50.602
2jh0701Prothrombin3.4.21.50.602
2zhe13UProthrombin3.4.21.50.602
1t4u81AProthrombin3.4.21.50.601
2zdv37UProthrombin3.4.21.50.600
2zff53UProthrombin3.4.21.50.600
1a4wQWEProthrombin3.4.21.50.599
1c4yIH3Prothrombin3.4.21.50.599
4baoMVFProthrombin3.4.21.50.596
4lxb7R9Prothrombin3.4.21.50.595
3c1kT15Prothrombin3.4.21.50.594
3c27DKKProthrombin3.4.21.50.594
3dux64UProthrombin3.4.21.50.594
1k22MELProthrombin3.4.21.50.593
1t4v14AProthrombin3.4.21.50.593
1sb1165Prothrombin3.4.21.50.591
2zg050UProthrombin3.4.21.50.591
1yplRA8Prothrombin3.4.21.50.588
2jh5895Prothrombin3.4.21.50.588
2jh6894Prothrombin3.4.21.50.588
4bakM67Prothrombin3.4.21.50.588
2uuj896Prothrombin3.4.21.50.586
1ypkCCRProthrombin3.4.21.50.585
1mueCDDProthrombin3.4.21.50.581
3biu10UProthrombin3.4.21.50.581
4ayy9MXProthrombin3.4.21.50.581
2bvs2CEProthrombin3.4.21.50.578
3qto10PProthrombin3.4.21.50.578
1ae8AZLProthrombin3.4.21.50.576
1zgi382Prothrombin3.4.21.50.576
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.574
1zrb062Prothrombin3.4.21.50.573
1ta6177Prothrombin3.4.21.50.569
2uuk897Prothrombin3.4.21.50.569
4rn615UProthrombin3.4.21.50.569
2cf8ESHProthrombin3.4.21.50.568
5cmx0G6Prothrombin3.4.21.50.565
2bxtC2DProthrombin3.4.21.50.564
1d3pBT3Prothrombin3.4.21.50.563
1z71L17Prothrombin3.4.21.50.562
3utu1TSProthrombin3.4.21.50.562
4bamMM9Prothrombin3.4.21.50.562
3qwc98PProthrombin3.4.21.50.561
1oytFSNProthrombin3.4.21.50.560
4az29MUProthrombin3.4.21.50.560
1afeALZProthrombin3.4.21.50.558
1vzqSHYProthrombin3.4.21.50.550
2cf9348Prothrombin3.4.21.50.540
1k21IGNProthrombin3.4.21.50.539
4e7r0NWProthrombin3.4.21.50.536
4banM6SProthrombin3.4.21.50.535
2cn0F25Prothrombin3.4.21.50.531
3qtv06PProthrombin3.4.21.50.528
1c4vIH2Prothrombin3.4.21.50.521
1w7gMIUProthrombin3.4.21.50.520
4baqM4ZProthrombin3.4.21.50.520
1o0d163Prothrombin3.4.21.50.511
1riwOSCProthrombin3.4.21.50.508
3dhk23UProthrombin3.4.21.50.504
4ayv9MQProthrombin3.4.21.50.502
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.487
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.483
2gdeSN3Prothrombin3.4.21.50.481
1umaIN2Prothrombin3.4.21.50.480
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.473
2ejvNADL-threonine 3-dehydrogenase/0.472
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.466
3adaNADSubunit alpha of sarocosine oxidase/0.464
3biv11UProthrombin3.4.21.50.463
3eksCY9Actin-5C/0.462
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.460
1pqc444Oxysterols receptor LXR-beta/0.459
1ghv120Prothrombin3.4.21.50.458
4gxs0YSGlutamate receptor 2/0.458
3vqsJT1Genome polyprotein/0.457
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.452
4jtqNAPAldo-keto reductase family 1 member C2/0.451
2ignFADPyranose 2-oxidase/0.450
4xguADPPutative pachytene checkpoint protein 2/0.450
1fmlRTLRetinol dehydratase/0.449
3vyfVYFRenin3.4.23.150.449
1w0kADPATP synthase subunit alpha, mitochondrial/0.448
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.448
2ziq26UProthrombin3.4.21.50.448
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.448
3oqkS52Renin3.4.23.150.448
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.448
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.446
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.445
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.445
4gh5NADShort-chain dehydrogenase/reductase SDR/0.445
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.445
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3oqfS51Renin3.4.23.150.444
1cf3FADGlucose oxidase1.1.3.40.443
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.443
1c1uBAIProthrombin3.4.21.50.442
2x7hPFNProstaglandin reductase 310.442
4x28FDAAcyl-CoA dehydrogenase FadE26/0.442
4x28FDAAcyl-CoA dehydrogenase FadE27/0.442
1kvrNADUDP-glucose 4-epimerase5.1.3.20.441
1mu8CDBProthrombin3.4.21.50.441
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3own3OWRenin3.4.23.150.440
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.440
4kbyC2EStimulator of interferon genes protein/0.440