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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
2bdyUNBProthrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2bdyUNBProthrombin3.4.21.51.000
1d4pBPPProthrombin3.4.21.50.703
4ax9N5NProthrombin3.4.21.50.678
2pksG44Prothrombin3.4.21.50.662
2r2mI50Prothrombin3.4.21.50.659
2zfr46UProthrombin3.4.21.50.658
2jh5895Prothrombin3.4.21.50.653
2uuk897Prothrombin3.4.21.50.649
1xm1GAHProthrombin3.4.21.50.646
1ypeUIPProthrombin3.4.21.50.646
1ypjUIBProthrombin3.4.21.50.646
1d9i00PProthrombin3.4.21.50.645
2anmCDOProthrombin3.4.21.50.645
2cf8ESHProthrombin3.4.21.50.645
1jwtBLIProthrombin3.4.21.50.642
1ypmRA4Prothrombin3.4.21.50.639
2zhq27UProthrombin3.4.21.50.639
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.639
2zi224UProthrombin3.4.21.50.637
3qwc98PProthrombin3.4.21.50.635
2zhf49UProthrombin3.4.21.50.634
1ta6177Prothrombin3.4.21.50.633
1d3pBT3Prothrombin3.4.21.50.631
2v3oI26Prothrombin3.4.21.50.631
1nm6L86Prothrombin3.4.21.50.628
1t4u81AProthrombin3.4.21.50.625
1t4v14AProthrombin3.4.21.50.621
1d3dBZTProthrombin3.4.21.50.618
1z71L17Prothrombin3.4.21.50.618
2zda32UProthrombin3.4.21.50.618
1c4yIH3Prothrombin3.4.21.50.615
2zfp19UProthrombin3.4.21.50.612
2zhw12UProthrombin3.4.21.50.611
2v3hI25Prothrombin3.4.21.50.608
1sb1165Prothrombin3.4.21.50.603
4ayy9MXProthrombin3.4.21.50.602
1ypgUIRProthrombin3.4.21.50.601
2jh6894Prothrombin3.4.21.50.601
4n3l2FNProthrombin3.4.21.50.601
2zfq45UProthrombin3.4.21.50.597
1mu6CDAProthrombin3.4.21.50.595
2gdeSN3Prothrombin3.4.21.50.594
2zgx29UProthrombin3.4.21.50.594
4bahMELProthrombin3.4.21.50.594
1c4uIH1Prothrombin3.4.21.50.593
3p1799PProthrombin3.4.21.50.593
1yplRA8Prothrombin3.4.21.50.592
1zgv501Prothrombin3.4.21.50.588
2cn0F25Prothrombin3.4.21.50.588
3utu1TSProthrombin3.4.21.50.586
3eq02TSProthrombin3.4.21.50.585
2zc922UProthrombin3.4.21.50.584
3biu10UProthrombin3.4.21.50.584
2zgb21UProthrombin3.4.21.50.582
1vzqSHYProthrombin3.4.21.50.579
4lxb7R9Prothrombin3.4.21.50.578
1oytFSNProthrombin3.4.21.50.577
2zdv37UProthrombin3.4.21.50.572
2znk31UProthrombin3.4.21.50.572
1zgi382Prothrombin3.4.21.50.571
2zg050UProthrombin3.4.21.50.571
3c1kT15Prothrombin3.4.21.50.571
2cf9348Prothrombin3.4.21.50.570
4e7r0NWProthrombin3.4.21.50.570
5cmx0G6Prothrombin3.4.21.50.570
4baoMVFProthrombin3.4.21.50.568
1ae8AZLProthrombin3.4.21.50.567
1mueCDDProthrombin3.4.21.50.567
2zhe13UProthrombin3.4.21.50.564
1d6w00RProthrombin3.4.21.50.563
3qto10PProthrombin3.4.21.50.563
2bvs2CEProthrombin3.4.21.50.561
2zf051UProthrombin3.4.21.50.558
2zff53UProthrombin3.4.21.50.558
1ypkCCRProthrombin3.4.21.50.554
2jh0701Prothrombin3.4.21.50.553
2uuj896Prothrombin3.4.21.50.551
3c27DKKProthrombin3.4.21.50.551
3qtv06PProthrombin3.4.21.50.550
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.549
1k22MELProthrombin3.4.21.50.546
4az29MUProthrombin3.4.21.50.542
1zrb062Prothrombin3.4.21.50.538
1k21IGNProthrombin3.4.21.50.536
3dux64UProthrombin3.4.21.50.534
1c4vIH2Prothrombin3.4.21.50.532
4bamMM9Prothrombin3.4.21.50.530
4bakM67Prothrombin3.4.21.50.529
1a4wQWEProthrombin3.4.21.50.527
1afeALZProthrombin3.4.21.50.527
1riwOSCProthrombin3.4.21.50.527
1nzq162Prothrombin3.4.21.50.519
2bxtC2DProthrombin3.4.21.50.518
4ayv9MQProthrombin3.4.21.50.518
1w7gMIUProthrombin3.4.21.50.513
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.495
4banM6SProthrombin3.4.21.50.492
3dhk23UProthrombin3.4.21.50.490
4baqM4ZProthrombin3.4.21.50.489
3adaNADSubunit alpha of sarocosine oxidase/0.477
1ktsC24Prothrombin3.4.21.50.475
4hfp15UProthrombin3.4.21.50.475
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.472
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.467
2dvlFADAcyl-CoA dehydrogenase/0.462
1o0d163Prothrombin3.4.21.50.459
2ziq26UProthrombin3.4.21.50.458
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.457
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.454
1mu8CDBProthrombin3.4.21.50.453
3tneRITCandidapepsin-13.4.23.240.452
1ghv120Prothrombin3.4.21.50.449
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.448
1c5nESIProthrombin3.4.21.50.446
2xveFADPutative flavin-containing monooxygenase/0.444
4bttVYRCoagulation factor X3.4.21.60.444
1pqc444Oxysterols receptor LXR-beta/0.443
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.443
5fm7ADPRuvB-like helicase/0.443
1fmlRTLRetinol dehydratase/0.442
3egkM18Prothrombin3.4.21.50.442
2b3dFADModulator of drug activity B/0.441
1bcuPRLProthrombin3.4.21.50.440
3qgf46FGenome polyprotein2.7.7.480.440
4bfxZVXPantothenate kinase2.7.1.330.440
4r81FMNPredicted NADH dehydrogenase/0.440