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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
1ypkCCRProthrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1ypkCCRProthrombin3.4.21.51.000
1d6w00RProthrombin3.4.21.50.745
1sb1165Prothrombin3.4.21.50.669
1yplRA8Prothrombin3.4.21.50.658
1ypmRA4Prothrombin3.4.21.50.647
1ypgUIRProthrombin3.4.21.50.646
1ae8AZLProthrombin3.4.21.50.641
2zfq45UProthrombin3.4.21.50.640
2v3oI26Prothrombin3.4.21.50.637
2zi224UProthrombin3.4.21.50.637
1d9i00PProthrombin3.4.21.50.636
2jh5895Prothrombin3.4.21.50.635
2znk31UProthrombin3.4.21.50.635
1a4wQWEProthrombin3.4.21.50.630
1c4yIH3Prothrombin3.4.21.50.627
1k21IGNProthrombin3.4.21.50.625
2zda32UProthrombin3.4.21.50.624
1mueCDDProthrombin3.4.21.50.623
2bvs2CEProthrombin3.4.21.50.623
2zc922UProthrombin3.4.21.50.623
1t4v14AProthrombin3.4.21.50.622
2jh6894Prothrombin3.4.21.50.619
4ayy9MXProthrombin3.4.21.50.617
2zg050UProthrombin3.4.21.50.612
4ax9N5NProthrombin3.4.21.50.611
1t4u81AProthrombin3.4.21.50.610
1oytFSNProthrombin3.4.21.50.607
1ypeUIPProthrombin3.4.21.50.604
2zfr46UProthrombin3.4.21.50.604
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.604
2zhq27UProthrombin3.4.21.50.603
2zhe13UProthrombin3.4.21.50.600
3eq02TSProthrombin3.4.21.50.598
1ypjUIBProthrombin3.4.21.50.594
3qwc98PProthrombin3.4.21.50.594
1zrb062Prothrombin3.4.21.50.593
3c1kT15Prothrombin3.4.21.50.593
1nzq162Prothrombin3.4.21.50.591
2cf8ESHProthrombin3.4.21.50.591
2cf9348Prothrombin3.4.21.50.591
4ayv9MQProthrombin3.4.21.50.591
2zhf49UProthrombin3.4.21.50.590
1z71L17Prothrombin3.4.21.50.588
4lxb7R9Prothrombin3.4.21.50.588
1mu6CDAProthrombin3.4.21.50.585
1zgi382Prothrombin3.4.21.50.585
2gdeSN3Prothrombin3.4.21.50.585
2r2mI50Prothrombin3.4.21.50.585
2uuk897Prothrombin3.4.21.50.585
1afeALZProthrombin3.4.21.50.583
2cn0F25Prothrombin3.4.21.50.583
4az29MUProthrombin3.4.21.50.583
1d4pBPPProthrombin3.4.21.50.580
1jwtBLIProthrombin3.4.21.50.580
2pksG44Prothrombin3.4.21.50.578
1nm6L86Prothrombin3.4.21.50.576
1xm1GAHProthrombin3.4.21.50.576
2zgx29UProthrombin3.4.21.50.576
4bamMM9Prothrombin3.4.21.50.576
4rn615UProthrombin3.4.21.50.576
1d3dBZTProthrombin3.4.21.50.574
2zf051UProthrombin3.4.21.50.574
3dux64UProthrombin3.4.21.50.573
1riwOSCProthrombin3.4.21.50.569
2anmCDOProthrombin3.4.21.50.565
2bdyUNBProthrombin3.4.21.50.564
2zdv37UProthrombin3.4.21.50.564
3biu10UProthrombin3.4.21.50.564
1vzqSHYProthrombin3.4.21.50.563
4e7r0NWProthrombin3.4.21.50.563
2zgb21UProthrombin3.4.21.50.562
4bakM67Prothrombin3.4.21.50.559
2jh0701Prothrombin3.4.21.50.558
2zff53UProthrombin3.4.21.50.557
1ta6177Prothrombin3.4.21.50.556
1c4uIH1Prothrombin3.4.21.50.554
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.553
2zhw12UProthrombin3.4.21.50.550
2uuj896Prothrombin3.4.21.50.548
1d3pBT3Prothrombin3.4.21.50.545
4banM6SProthrombin3.4.21.50.545
2zfp19UProthrombin3.4.21.50.542
3p1799PProthrombin3.4.21.50.542
3qto10PProthrombin3.4.21.50.540
4baqM4ZProthrombin3.4.21.50.534
3c27DKKProthrombin3.4.21.50.532
4baoMVFProthrombin3.4.21.50.532
1k22MELProthrombin3.4.21.50.527
4n3l2FNProthrombin3.4.21.50.527
1zgv501Prothrombin3.4.21.50.524
2v3hI25Prothrombin3.4.21.50.521
4bahMELProthrombin3.4.21.50.519
2bxtC2DProthrombin3.4.21.50.518
1w7gMIUProthrombin3.4.21.50.510
1uvsI11Prothrombin3.4.21.50.508
3qtv06PProthrombin3.4.21.50.507
3biv11UProthrombin3.4.21.50.506
2ziq26UProthrombin3.4.21.50.504
5cmx0G6Prothrombin3.4.21.50.504
4hfp15UProthrombin3.4.21.50.496
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.489
3utu1TSProthrombin3.4.21.50.479
3dhk23UProthrombin3.4.21.50.474
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.473
2a2xNA9Prothrombin3.4.21.50.472
3egkM18Prothrombin3.4.21.50.467
1ghv120Prothrombin3.4.21.50.464
1mu8CDBProthrombin3.4.21.50.463
1o0d163Prothrombin3.4.21.50.463
1c4vIH2Prothrombin3.4.21.50.461
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
4loy6XSProthrombin3.4.21.50.455
3vqsJT1Genome polyprotein/0.452
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
2iqgF2IBeta-secretase 13.4.23.460.450
1umaIN2Prothrombin3.4.21.50.448
1xe55FEPlasmepsin-23.4.23.390.447
4a802ANMajor pollen allergen Bet v 1-A/0.447
2ignFADPyranose 2-oxidase/0.446
4azy7F3Beta-secretase 13.4.23.460.445
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.445
4xguADPPutative pachytene checkpoint protein 2/0.445
1c7oPPGHemolysin/0.442
2b8l5HABeta-secretase 13.4.23.460.442
2gjlFMNNitronate monooxygenase1.13.12.160.442
4bgiI4IEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.442
1cjkFOKAdenylate cyclase type 2/0.441
1cjkFOKAdenylate cyclase type 5/0.441
1o5gCR9Prothrombin3.4.21.50.441
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3oqkS52Renin3.4.23.150.440
4kbyC2EStimulator of interferon genes protein/0.440