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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
2zdv37UProthrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2zdv37UProthrombin3.4.21.51.000
2zff53UProthrombin3.4.21.50.872
2zgx29UProthrombin3.4.21.50.862
2zda32UProthrombin3.4.21.50.847
2zc922UProthrombin3.4.21.50.841
2znk31UProthrombin3.4.21.50.811
2zfr46UProthrombin3.4.21.50.803
2zhf49UProthrombin3.4.21.50.803
2zg050UProthrombin3.4.21.50.800
2zi224UProthrombin3.4.21.50.796
3biu10UProthrombin3.4.21.50.782
2zhe13UProthrombin3.4.21.50.780
3eq02TSProthrombin3.4.21.50.770
2zgb21UProthrombin3.4.21.50.766
3dux64UProthrombin3.4.21.50.763
2zhq27UProthrombin3.4.21.50.759
4ax9N5NProthrombin3.4.21.50.754
2zfp19UProthrombin3.4.21.50.748
2zf051UProthrombin3.4.21.50.739
4bamMM9Prothrombin3.4.21.50.731
3biv11UProthrombin3.4.21.50.729
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.723
2zfq45UProthrombin3.4.21.50.720
1ypgUIRProthrombin3.4.21.50.703
3qto10PProthrombin3.4.21.50.696
4bakM67Prothrombin3.4.21.50.696
1d3dBZTProthrombin3.4.21.50.695
3dhk23UProthrombin3.4.21.50.695
3p1799PProthrombin3.4.21.50.694
2r2mI50Prothrombin3.4.21.50.691
2zhw12UProthrombin3.4.21.50.686
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.686
1d4pBPPProthrombin3.4.21.50.682
1ypeUIPProthrombin3.4.21.50.680
1ypjUIBProthrombin3.4.21.50.676
1c4uIH1Prothrombin3.4.21.50.675
1d6w00RProthrombin3.4.21.50.672
2v3oI26Prothrombin3.4.21.50.670
3c27DKKProthrombin3.4.21.50.668
1mueCDDProthrombin3.4.21.50.666
1zrb062Prothrombin3.4.21.50.660
2anmCDOProthrombin3.4.21.50.659
2ziq26UProthrombin3.4.21.50.658
4bahMELProthrombin3.4.21.50.656
4baoMVFProthrombin3.4.21.50.656
2jh5895Prothrombin3.4.21.50.654
1t4v14AProthrombin3.4.21.50.653
1t4u81AProthrombin3.4.21.50.652
4banM6SProthrombin3.4.21.50.652
1k21IGNProthrombin3.4.21.50.651
1ae8AZLProthrombin3.4.21.50.648
2pksG44Prothrombin3.4.21.50.648
4baqM4ZProthrombin3.4.21.50.648
1ypmRA4Prothrombin3.4.21.50.647
1nm6L86Prothrombin3.4.21.50.646
2bdyUNBProthrombin3.4.21.50.646
1afeALZProthrombin3.4.21.50.643
1sb1165Prothrombin3.4.21.50.643
1xm1GAHProthrombin3.4.21.50.641
2uuk897Prothrombin3.4.21.50.640
1mu6CDAProthrombin3.4.21.50.639
3qwc98PProthrombin3.4.21.50.638
1yplRA8Prothrombin3.4.21.50.633
1z71L17Prothrombin3.4.21.50.630
1zgv501Prothrombin3.4.21.50.630
4n3l2FNProthrombin3.4.21.50.628
3c1kT15Prothrombin3.4.21.50.620
1c4yIH3Prothrombin3.4.21.50.619
1d9i00PProthrombin3.4.21.50.619
1jwtBLIProthrombin3.4.21.50.619
3qtv06PProthrombin3.4.21.50.618
1d3pBT3Prothrombin3.4.21.50.616
2bvs2CEProthrombin3.4.21.50.615
4lxb7R9Prothrombin3.4.21.50.613
1ta6177Prothrombin3.4.21.50.612
1vzqSHYProthrombin3.4.21.50.612
2jh0701Prothrombin3.4.21.50.612
2jh6894Prothrombin3.4.21.50.612
1oytFSNProthrombin3.4.21.50.603
2uuj896Prothrombin3.4.21.50.603
3utu1TSProthrombin3.4.21.50.600
2v3hI25Prothrombin3.4.21.50.599
4ayy9MXProthrombin3.4.21.50.598
4e7r0NWProthrombin3.4.21.50.598
1k22MELProthrombin3.4.21.50.595
1ypkCCRProthrombin3.4.21.50.594
4az29MUProthrombin3.4.21.50.582
2cn0F25Prothrombin3.4.21.50.581
1zgi382Prothrombin3.4.21.50.578
1nzq162Prothrombin3.4.21.50.573
1a4wQWEProthrombin3.4.21.50.572
2cf9348Prothrombin3.4.21.50.572
1w7gMIUProthrombin3.4.21.50.566
1o0d163Prothrombin3.4.21.50.562
1c4vIH2Prothrombin3.4.21.50.559
2cf8ESHProthrombin3.4.21.50.557
1mu8CDBProthrombin3.4.21.50.553
4rn615UProthrombin3.4.21.50.553
2gdeSN3Prothrombin3.4.21.50.552
3egkM18Prothrombin3.4.21.50.549
2bxtC2DProthrombin3.4.21.50.542
3f6891UProthrombin3.4.21.50.540
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.536
4hfp15UProthrombin3.4.21.50.532
1ghv120Prothrombin3.4.21.50.526
1ta2176Prothrombin3.4.21.50.524
1uvsI11Prothrombin3.4.21.50.521
1riwOSCProthrombin3.4.21.50.520
5cmx0G6Prothrombin3.4.21.50.520
4ayv9MQProthrombin3.4.21.50.514
4loy6XSProthrombin3.4.21.50.500
1umaIN2Prothrombin3.4.21.50.492
2a2xNA9Prothrombin3.4.21.50.492
1c5nESIProthrombin3.4.21.50.491
1ktsC24Prothrombin3.4.21.50.490
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.483
1bcuPRLProthrombin3.4.21.50.481
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.478
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.478
4q71FADBifunctional protein PutA/0.478
1j9zFADNADPH--cytochrome P450 reductase/0.477
4b1jA1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.476
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.476
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.470
3qgf46FGenome polyprotein2.7.7.480.469
4a802ANMajor pollen allergen Bet v 1-A/0.469
4ey6GNTAcetylcholinesterase3.1.1.70.469
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.469
1sl3170Prothrombin3.4.21.50.468
2xuoTZ4Acetylcholinesterase3.1.1.70.468
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.468
4kbyC2EStimulator of interferon genes protein/0.467
1pq944BOxysterols receptor LXR-beta/0.466
2g1r3IGRenin3.4.23.150.465
5dozNDPJamJ/0.465
3adaNADSubunit alpha of sarocosine oxidase/0.464
3eksCY9Actin-5C/0.464
3q7fED2Uncharacterized protein/0.464
2g1s4IGRenin3.4.23.150.463
3own3OWRenin3.4.23.150.463
3oqfS51Renin3.4.23.150.462
2g1y5IGRenin3.4.23.150.461
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.461
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.461
3vqsJT1Genome polyprotein/0.460
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.458
3oqkS52Renin3.4.23.150.458
2g1o2IGRenin3.4.23.150.457
2g226IGRenin3.4.23.150.457
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.457
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.456
1x8lOXRRetinol dehydratase/0.456
2g8yNADHydroxycarboxylate dehydrogenase B/0.456
2rlcCHDCholoylglycine hydrolase3.5.1.240.456
4a862ANMajor pollen allergen Bet v 1-A/0.456
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.456
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.456
1u1gBBBUridine phosphorylase2.4.2.30.455
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.455
3ekuCY9Actin-5C/0.455
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.455
5c3aURMHisto-blood group ABO system transferase/0.455
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.454
1rneC60Renin3.4.23.150.454
2po7CHDFerrochelatase, mitochondrial4.99.1.10.454
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.454
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.454
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.454
1gj4132Prothrombin3.4.21.50.453
1pqc444Oxysterols receptor LXR-beta/0.453
2ha6SCKAcetylcholinesterase3.1.1.70.453
2xuhTZ4Acetylcholinesterase3.1.1.70.453
2cbqTH2Neocarzinostatin/0.452
2qimZEAClass 10 plant pathogenesis-related protein/0.452
2wu4HBPAcetylcholinesterase3.1.1.70.452
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.452
4fsl0VBBeta-secretase 13.4.23.460.452
3wqmB29Diterpene synthase3.1.7.80.451
4epq0RRPoly(ADP-ribose) glycohydrolase/0.451
4k8s1QTBeta-secretase 13.4.23.460.451
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.451
1bil0IURenin3.4.23.150.450
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.450
1ohhANPATP synthase subunit alpha, mitochondrial/0.450
1ohhANPATP synthase subunit beta, mitochondrial3.6.3.140.450
2q153MRBeta-secretase 13.4.23.460.450
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.450
2xuiTZ5Acetylcholinesterase3.1.1.70.450
2xukTZ5Acetylcholinesterase3.1.1.70.450
2xupTZ5Acetylcholinesterase3.1.1.70.450
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.450
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.450
1cs4FOKAdenylate cyclase type 2/0.449
1cs4FOKAdenylate cyclase type 5/0.449
2vbdV10Isopenicillin N synthase1.21.3.10.449
4h6pFMNChromate reductase/0.449
1c1uBAIProthrombin3.4.21.50.448
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.448
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.448
4arbC57Acetylcholinesterase3.1.1.70.448
4c5oFADPutative monooxygenase/0.448
4jtqNAPAldo-keto reductase family 1 member C2/0.448
5cyoGDPSeptin-9/0.448
2b8l5HABeta-secretase 13.4.23.460.447
2wf1ZY1Beta-secretase 13.4.23.460.447
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3qe2FMNNADPH--cytochrome P450 reductase/0.447
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.447
1w0kADPATP synthase subunit alpha, mitochondrial/0.446
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.446
2ignFADPyranose 2-oxidase/0.446
2rqfJH3Hemolymph juvenile hormone binding protein/0.446
3ksqZ96Protein farnesyltransferase subunit beta2.5.1.580.446
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.446
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.446
4ejmNAPPutative zinc-binding dehydrogenase/0.446
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.446
4lzwTHMUridine phosphorylase/0.446
1fmlRTLRetinol dehydratase/0.445
2g1n1IGRenin3.4.23.150.445
4bfxZVXPantothenate kinase2.7.1.330.445
4kwcSAHMethyltransferase domain family/0.445
2cndFADNitrate reductase [NADH]1.7.1.10.444
2ptfFMNUncharacterized protein MTH_863/0.444
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.444
3sfy3FYUncharacterized protein/0.444
4bttVYRCoagulation factor X3.4.21.60.444
4dpi0N1Beta-secretase 13.4.23.460.444
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.444
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.444
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.444
4uthFMNXenobiotic reductase/0.444
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
1o1t2NHProtein farnesyltransferase subunit beta2.5.1.580.443
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.443
2il2LIXRenin3.4.23.150.443
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.443
3g70A5TRenin3.4.23.150.443
4lxa1YSBeta-secretase 13.4.23.460.443
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.443
5irnADPNucleotide binding oligomerization domain containing 2/0.443
1upw444Oxysterols receptor LXR-beta/0.442
1wqvPSMCoagulation factor VII3.4.21.210.442
2j3qTFLAcetylcholinesterase3.1.1.70.442
2viyVG3Beta-secretase 13.4.23.460.442
2vnnCM7Beta-secretase 13.4.23.460.442
2xvhNAPPutative flavin-containing monooxygenase/0.442
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.442
3oadLPORenin3.4.23.150.442
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.442
4a87NARMajor pollen allergen Bet v 1-A/0.442
4e2bFMNDehydrogenase/0.442
1x7hNDPPutative ketoacyl reductase1.3.10.441
1xs7MMIBeta-secretase 13.4.23.460.441
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.441
2vyqFADFerredoxin--NADP reductase1.18.1.20.441
3vyeVYERenin3.4.23.150.441
4gxs0YSGlutamate receptor 2/0.441
4xbjIN5Alanine racemase, biosynthetic/0.441
1ja0FADNADPH--cytochrome P450 reductase/0.440
2wf4ZY4Beta-secretase 13.4.23.460.440
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.440
2zevIPEGeranylgeranyl pyrophosphate synthase/0.440
3e30ED4Protein farnesyltransferase subunit beta2.5.1.580.440
3vilSA0Beta-glucosidase/0.440
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440