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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2pksG44Prothrombin3.4.21.5

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2pksG44Prothrombin3.4.21.51.000
2bdyUNBProthrombin3.4.21.50.689
1ypmRA4Prothrombin3.4.21.50.663
2zhq27UProthrombin3.4.21.50.661
1d6w00RProthrombin3.4.21.50.657
2zgx29UProthrombin3.4.21.50.642
2r2mI50Prothrombin3.4.21.50.638
1jwtBLIProthrombin3.4.21.50.636
2zhw12UProthrombin3.4.21.50.635
2zgb21UProthrombin3.4.21.50.632
1ypjUIBProthrombin3.4.21.50.631
4ax9N5NProthrombin3.4.21.50.631
2v3oI26Prothrombin3.4.21.50.630
1zgv501Prothrombin3.4.21.50.623
2zc922UProthrombin3.4.21.50.622
2zda32UProthrombin3.4.21.50.622
2zfp19UProthrombin3.4.21.50.621
2anmCDOProthrombin3.4.21.50.618
3eq02TSProthrombin3.4.21.50.617
1mu6CDAProthrombin3.4.21.50.615
1t4u81AProthrombin3.4.21.50.615
1nzq162Prothrombin3.4.21.50.614
4bahMELProthrombin3.4.21.50.614
2zhf49UProthrombin3.4.21.50.612
2zf051UProthrombin3.4.21.50.611
1ypeUIPProthrombin3.4.21.50.610
2zi224UProthrombin3.4.21.50.610
2v3hI25Prothrombin3.4.21.50.609
2zfr46UProthrombin3.4.21.50.608
2zfq45UProthrombin3.4.21.50.607
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.607
4n3l2FNProthrombin3.4.21.50.606
1d3dBZTProthrombin3.4.21.50.605
1ypgUIRProthrombin3.4.21.50.605
3p1799PProthrombin3.4.21.50.605
1d9i00PProthrombin3.4.21.50.604
2znk31UProthrombin3.4.21.50.604
2zhe13UProthrombin3.4.21.50.603
1d4pBPPProthrombin3.4.21.50.602
1t4v14AProthrombin3.4.21.50.600
1a4wQWEProthrombin3.4.21.50.599
1gj5130Prothrombin3.4.21.50.599
2zdv37UProthrombin3.4.21.50.599
2zff53UProthrombin3.4.21.50.599
1xm1GAHProthrombin3.4.21.50.597
3dux64UProthrombin3.4.21.50.597
1c4uIH1Prothrombin3.4.21.50.596
4baoMVFProthrombin3.4.21.50.596
3c1kT15Prothrombin3.4.21.50.595
1ghv120Prothrombin3.4.21.50.594
3c27DKKProthrombin3.4.21.50.594
1nm6L86Prothrombin3.4.21.50.592
1sb1165Prothrombin3.4.21.50.591
2zg050UProthrombin3.4.21.50.591
4bakM67Prothrombin3.4.21.50.588
1c4yIH3Prothrombin3.4.21.50.587
1yplRA8Prothrombin3.4.21.50.586
2uuj896Prothrombin3.4.21.50.586
1ypkCCRProthrombin3.4.21.50.585
1o2g696Prothrombin3.4.21.50.584
1k22MELProthrombin3.4.21.50.583
1mueCDDProthrombin3.4.21.50.581
3biu10UProthrombin3.4.21.50.581
4ayy9MXProthrombin3.4.21.50.581
2jh5895Prothrombin3.4.21.50.580
2jh6894Prothrombin3.4.21.50.580
3qto10PProthrombin3.4.21.50.578
1ae8AZLProthrombin3.4.21.50.576
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.574
1zgi382Prothrombin3.4.21.50.573
1zrb062Prothrombin3.4.21.50.573
2uuk897Prothrombin3.4.21.50.566
1afeALZProthrombin3.4.21.50.565
1z71L17Prothrombin3.4.21.50.565
2bxtC2DProthrombin3.4.21.50.564
3utu1TSProthrombin3.4.21.50.562
4bamMM9Prothrombin3.4.21.50.562
5cmx0G6Prothrombin3.4.21.50.561
1d3pBT3Prothrombin3.4.21.50.559
2cf8ESHProthrombin3.4.21.50.559
3qwc98PProthrombin3.4.21.50.558
1ta6177Prothrombin3.4.21.50.557
1umaIN2Prothrombin3.4.21.50.556
1oytFSNProthrombin3.4.21.50.552
1vzqSHYProthrombin3.4.21.50.550
1bcuPRLProthrombin3.4.21.50.543
1c1uBAIProthrombin3.4.21.50.542
1k21IGNProthrombin3.4.21.50.539
4banM6SProthrombin3.4.21.50.535
4e7r0NWProthrombin3.4.21.50.534
2cf9348Prothrombin3.4.21.50.533
3qtv06PProthrombin3.4.21.50.528
1o5gCR9Prothrombin3.4.21.50.527
1c4vIH2Prothrombin3.4.21.50.523
4baqM4ZProthrombin3.4.21.50.520
1w7gMIUProthrombin3.4.21.50.516
1o0d163Prothrombin3.4.21.50.511
1riwOSCProthrombin3.4.21.50.507
4ayv9MQProthrombin3.4.21.50.499
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.478
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.473
4az29MUProthrombin3.4.21.50.465
3biv11UProthrombin3.4.21.50.463
3eksCY9Actin-5C/0.461
4jtqNAPAldo-keto reductase family 1 member C2/0.460
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.459
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.458
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.458
1c5nESIProthrombin3.4.21.50.454
3vy2FMNFMN-binding protein/0.454
1gj4132Prothrombin3.4.21.50.453
2ejvNADL-threonine 3-dehydrogenase/0.453
1d2hSAHGlycine N-methyltransferase2.1.1.200.452
3nmpPYVAbscisic acid receptor PYL2/0.452
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.451
1pqc444Oxysterols receptor LXR-beta/0.450
2g8yNADHydroxycarboxylate dehydrogenase B/0.449
3fhxPLPPyridoxal kinase2.7.1.350.449
3vyfVYFRenin3.4.23.150.449
4ey6GNTAcetylcholinesterase3.1.1.70.449
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.448
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.448
1w0kADPATP synthase subunit alpha, mitochondrial/0.447
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.447
2ziq26UProthrombin3.4.21.50.447
3mauPLRPutative sphingosine-1-phosphate lyase/0.446
4euaCOASuccinyl-CoA:acetate CoA-transferase/0.446
2bxoOPBSerum albumin/0.445
3adaNADSubunit alpha of sarocosine oxidase/0.445
1mu8CDBProthrombin3.4.21.50.444
4c73TLH3-oxoacyl-ACP synthase/0.444
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.443
4gxs0YSGlutamate receptor 2/0.443
1fmlRTLRetinol dehydratase/0.442
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3ou2SAHSAM-dependent methyltransferase/0.442
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.441
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.441
2c29NAPDihydroflavonol 4-reductase/0.441
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
2zevIPEGeranylgeranyl pyrophosphate synthase/0.440
3vqsJT1Genome polyprotein/0.440
4b4w9L9Bifunctional protein FolD/0.440
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.440