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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
4bahMELProthrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4bahMELProthrombin3.4.21.51.000
2zgb21UProthrombin3.4.21.50.820
2zhq27UProthrombin3.4.21.50.768
4baoMVFProthrombin3.4.21.50.765
3eq02TSProthrombin3.4.21.50.743
4bamMM9Prothrombin3.4.21.50.732
4bakM67Prothrombin3.4.21.50.731
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.730
2zhw12UProthrombin3.4.21.50.728
2zf051UProthrombin3.4.21.50.720
2zhe13UProthrombin3.4.21.50.703
2anmCDOProthrombin3.4.21.50.702
1k22MELProthrombin3.4.21.50.701
2zhf49UProthrombin3.4.21.50.700
2zff53UProthrombin3.4.21.50.697
2pksG44Prothrombin3.4.21.50.693
4banM6SProthrombin3.4.21.50.693
2zfr46UProthrombin3.4.21.50.692
2zda32UProthrombin3.4.21.50.690
3qto10PProthrombin3.4.21.50.685
1d3dBZTProthrombin3.4.21.50.684
2r2mI50Prothrombin3.4.21.50.684
3p1799PProthrombin3.4.21.50.684
2bdyUNBProthrombin3.4.21.50.683
2zgx29UProthrombin3.4.21.50.683
2zdv37UProthrombin3.4.21.50.681
3dux64UProthrombin3.4.21.50.680
4baqM4ZProthrombin3.4.21.50.680
2znk31UProthrombin3.4.21.50.679
2zc922UProthrombin3.4.21.50.675
1ypmRA4Prothrombin3.4.21.50.674
1c4uIH1Prothrombin3.4.21.50.670
3qtv06PProthrombin3.4.21.50.664
1nm6L86Prothrombin3.4.21.50.662
2zfp19UProthrombin3.4.21.50.644
2v3oI26Prothrombin3.4.21.50.642
1d4pBPPProthrombin3.4.21.50.640
1sb1165Prothrombin3.4.21.50.638
1d3pBT3Prothrombin3.4.21.50.632
2v3hI25Prothrombin3.4.21.50.629
4n3l2FNProthrombin3.4.21.50.629
3qwc98PProthrombin3.4.21.50.628
2zg050UProthrombin3.4.21.50.627
1jwtBLIProthrombin3.4.21.50.624
1ypjUIBProthrombin3.4.21.50.620
1zrb062Prothrombin3.4.21.50.619
2uuj896Prothrombin3.4.21.50.618
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.618
2uuk897Prothrombin3.4.21.50.617
3dhk23UProthrombin3.4.21.50.617
4ax9N5NProthrombin3.4.21.50.617
1xm1GAHProthrombin3.4.21.50.616
1vzqSHYProthrombin3.4.21.50.614
3c27DKKProthrombin3.4.21.50.614
1ypeUIPProthrombin3.4.21.50.611
3biu10UProthrombin3.4.21.50.611
1d9i00PProthrombin3.4.21.50.609
3c1kT15Prothrombin3.4.21.50.609
2jh5895Prothrombin3.4.21.50.606
1zgi382Prothrombin3.4.21.50.604
1ta6177Prothrombin3.4.21.50.602
2zi224UProthrombin3.4.21.50.601
2cf8ESHProthrombin3.4.21.50.600
2zfq45UProthrombin3.4.21.50.599
1ae8AZLProthrombin3.4.21.50.598
1d6w00RProthrombin3.4.21.50.592
4ayy9MXProthrombin3.4.21.50.592
1oytFSNProthrombin3.4.21.50.589
1t4v14AProthrombin3.4.21.50.588
1z71L17Prothrombin3.4.21.50.588
2bxtC2DProthrombin3.4.21.50.588
1mu6CDAProthrombin3.4.21.50.586
1ypgUIRProthrombin3.4.21.50.586
4lxb7R9Prothrombin3.4.21.50.583
1c4yIH3Prothrombin3.4.21.50.582
1zgv501Prothrombin3.4.21.50.582
1afeALZProthrombin3.4.21.50.581
1k21IGNProthrombin3.4.21.50.581
2jh6894Prothrombin3.4.21.50.580
1a4wQWEProthrombin3.4.21.50.578
1t4u81AProthrombin3.4.21.50.578
2jh0701Prothrombin3.4.21.50.570
5cmx0G6Prothrombin3.4.21.50.569
1yplRA8Prothrombin3.4.21.50.565
2cf9348Prothrombin3.4.21.50.565
1ypkCCRProthrombin3.4.21.50.564
1nzq162Prothrombin3.4.21.50.563
2cn0F25Prothrombin3.4.21.50.563
1mueCDDProthrombin3.4.21.50.561
1w7gMIUProthrombin3.4.21.50.558
3utu1TSProthrombin3.4.21.50.550
2bvs2CEProthrombin3.4.21.50.543
4az29MUProthrombin3.4.21.50.530
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.526
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.524
1ghv120Prothrombin3.4.21.50.519
1o0d163Prothrombin3.4.21.50.519
3biv11UProthrombin3.4.21.50.509
3ekuCY9Actin-5C/0.508
2gdeSN3Prothrombin3.4.21.50.502
4gxs0YSGlutamate receptor 2/0.495
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.493
3oqfS51Renin3.4.23.150.490
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.485
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.484
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.482
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.482
2il2LIXRenin3.4.23.150.481
2pcaSAHDiphthine synthase/0.481
1j9zFADNADPH--cytochrome P450 reductase/0.480
2g1y5IGRenin3.4.23.150.479
2uxoTACHTH-type transcriptional regulator TtgR/0.479
2ziq26UProthrombin3.4.21.50.479
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.478
1culFOKAdenylate cyclase type 2/0.475
1culFOKAdenylate cyclase type 5/0.475
2rlcCHDCholoylglycine hydrolase3.5.1.240.475
1umaIN2Prothrombin3.4.21.50.474
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.474
2wu4HBPAcetylcholinesterase3.1.1.70.474
1ktsC24Prothrombin3.4.21.50.473
3c15FOKAdenylate cyclase type 2/0.472
3c15FOKAdenylate cyclase type 5/0.472
3phiNDPShikimate dehydrogenase (NADP(+))/0.472
4mlp2CXCryptochrome-2/0.472
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.471
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.470
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.470
2dv3SAHDiphthine synthase/0.469
4loy6XSProthrombin3.4.21.50.469
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.468
4bfxZVXPantothenate kinase2.7.1.330.468
4oztP1AEcdysone receptor, putative/0.467
2gv8NDPThiol-specific monooxygenase1.14.130.466
2ifaFMNUncharacterized protein/0.466
2gesCOKPantothenate kinase2.7.1.330.465
2igoFADPyranose 2-oxidase/0.465
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.465
3kpbSAMUncharacterized protein MJ0100/0.464
4jtqNAPAldo-keto reductase family 1 member C2/0.464
1riwOSCProthrombin3.4.21.50.463
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.463
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.463
1r2jFADFkbI/0.462
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.462
2bjfDXCCholoylglycine hydrolase3.5.1.240.462
2dvlFADAcyl-CoA dehydrogenase/0.462
2eldSAHDiphthine synthase/0.462
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
4kbyC2EStimulator of interferon genes protein/0.462
1cf3FADGlucose oxidase1.1.3.40.461
1cs4FOKAdenylate cyclase type 2/0.461
1cs4FOKAdenylate cyclase type 5/0.461
2ignFADPyranose 2-oxidase/0.460
3fhxPXLPyridoxal kinase2.7.1.350.460
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.460
4ayv9MQProthrombin3.4.21.50.460
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.459
3c3xNAPEugenol synthase 11.1.1.3180.459
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.459
4i1c1BEBeta-secretase 13.4.23.460.459
2rh1CAUBeta-2 adrenergic receptor/0.459
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.458
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3k4nFADPyranose 2-oxidase/0.458
3qt62P0Mevalonate diphosphate decarboxylase/0.458
4de10J6Beta-lactamase/0.458
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.458
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.457
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.456
2g1r3IGRenin3.4.23.150.456
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4uugPXGBranched-chain amino acid aminotransferase, putative/0.456
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.456
5irnADPNucleotide binding oligomerization domain containing 2/0.456
1ja0FADNADPH--cytochrome P450 reductase/0.455
2geuCOKPantothenate kinase2.7.1.330.455
3d91REMRenin3.4.23.150.455
3fr5I4AFatty acid-binding protein, adipocyte/0.455
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.455
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.455
4ips1G4Mycocyclosin synthase1.14.21.90.455
1mu8CDBProthrombin3.4.21.50.454
2znnS44Peroxisome proliferator-activated receptor alpha/0.454
3b6pTMPThree-prime repair exonuclease 13.1.11.20.454
3oqkS52Renin3.4.23.150.454
4dpf0LGBeta-secretase 13.4.23.460.454
4i1nFOLDihydrofolate reductase1.5.1.30.454
1c1uBAIProthrombin3.4.21.50.453
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.453
2ylzFADPhenylacetone monooxygenase1.14.13.920.453
3eigMTXDihydrofolate reductase1.5.1.30.453
1x8lOXRRetinol dehydratase/0.452
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.452
2vbpVB1Isopenicillin N synthase1.21.3.10.452
2wf1ZY1Beta-secretase 13.4.23.460.452
3qviK95HAP protein/0.452
4bb3KKAIsopenicillin N synthase1.21.3.10.452
1nhqFADNADH peroxidase1.11.1.10.451
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.451
1xe65FPPlasmepsin-23.4.23.390.451
3s5wNAPL-ornithine N(5)-monooxygenase/0.451
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.450
1pqc444Oxysterols receptor LXR-beta/0.450
3adaNADSubunit alpha of sarocosine oxidase/0.450
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3ha5SFGHydroxymycolate synthase MmaA42.1.10.450
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.450
4cdmFO1Deoxyribodipyrimidine photolyase/0.450
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.450
1c7oPPGHemolysin/0.449
2z4y252Geranylgeranyl pyrophosphate synthase/0.449
3bg7FADPyranose 2-oxidase/0.449
3fbuCOAAcetyltransferase, GNAT family/0.449
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.449
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.449
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
4yal2AMNADPH--cytochrome P450 reductase/0.449
1b2lNDCAlcohol dehydrogenase1.1.1.10.448
1ta2176Prothrombin3.4.21.50.448
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.448
2xvhNAPPutative flavin-containing monooxygenase/0.448
2z3nPHE_ARG_TYR_LEU_GLYLeucyl/phenylalanyl-tRNA--protein transferase2.3.2.60.448
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.448
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.448
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.447
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.447
2r8pT6FTransketolase 1/0.447
2w6qOA5Biotin carboxylase6.3.4.140.447
3oeeANPATP synthase subunit alpha, mitochondrial/0.447
3oeeANPATP synthase subunit beta, mitochondrial3.6.3.140.447
4psbGA3Cytokinin-specific binding protein/0.447
2x6o2TCTetracycline repressor protein class D/0.446
2ym1FADPhenylacetone monooxygenase1.14.13.920.446
3ska053Genome polyprotein2.7.7.480.446
3vqsJT1Genome polyprotein/0.446
3wbzATPtRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980}/0.446
4bftZVTPantothenate kinase2.7.1.330.446
1kkq471Peroxisome proliferator-activated receptor alpha/0.445
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.445
2pb5SAHDiphthine synthase/0.445
2wzySQXSoluble acetylcholine receptor/0.445
3br3ETHTH-type transcriptional regulator QacR/0.445
3eksCY9Actin-5C/0.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.445
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.444
1sozVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.444
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2huqSAHDiphthine synthase/0.444
2ikuLIYRenin3.4.23.150.444
2zbaZBATrichothecene 3-O-acetyltransferase/0.444
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.444
3fhxPLPPyridoxal kinase2.7.1.350.444
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4xguADPPutative pachytene checkpoint protein 2/0.444
4y9uNAPNADPH--cytochrome P450 reductase/0.444
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.444
1galFADGlucose oxidase1.1.3.40.443
1gvhFADFlavohemoprotein/0.443
1upw444Oxysterols receptor LXR-beta/0.443
2ej2PPEBranched-chain amino acid aminotransferase (IlvE)/0.443
2xlpNAPPutative flavin-containing monooxygenase/0.443
2zreAGSProtein RecA/0.443
3gobHXXDdmC/0.443
3ig6438Urokinase-type plasminogen activator3.4.21.730.443
3o6o94MHeat shock protein 83/0.443
3owaFADAcyl-CoA dehydrogenase/0.443
3upi0C2Genome polyprotein2.7.7.480.443
4a87NARMajor pollen allergen Bet v 1-A/0.443
4b0cC9H3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase4.2.1.590.443
4zm6ACON-acetyl-beta-D glucosaminidase/0.443
5choFADFlavin reductase/0.443
1pq944BOxysterols receptor LXR-beta/0.442
2gvdFKPAdenylate cyclase type 2/0.442
2gvdFKPAdenylate cyclase type 5/0.442
2po7CHDFerrochelatase, mitochondrial4.99.1.10.442
2xuoTZ4Acetylcholinesterase3.1.1.70.442
3vilSA0Beta-glucosidase/0.442
3zoiM2WIsopenicillin N synthase1.21.3.10.442
4arbC57Acetylcholinesterase3.1.1.70.442
4dju0KKBeta-secretase 13.4.23.460.442
4yau2AMNADPH--cytochrome P450 reductase/0.442
5d6lCAUBeta-2 adrenergic receptor/0.442
1dghNDPCatalase1.11.1.60.441
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.441
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3maaFKPAdenylate cyclase type 2/0.441
3maaFKPAdenylate cyclase type 5/0.441
4b7754MBeta-secretase 13.4.23.460.441
4g6hNAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.441
1fmjRTLRetinol dehydratase/0.440
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1oc1ASVIsopenicillin N synthase1.21.3.10.440
2bu9HFVIsopenicillin N synthase1.21.3.10.440
2pchSAHDiphthine synthase/0.440
2zevIPEGeranylgeranyl pyrophosphate synthase/0.440
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
4b1e6T6Beta-secretase 13.4.23.460.440
4c5oFADPutative monooxygenase/0.440
4de00JBBeta-lactamase/0.440
4rn615UProthrombin3.4.21.50.440
4xmxBESAminopeptidase N3.4.11.20.440
4yaw2AMNADPH--cytochrome P450 reductase/0.440
5jscFADPutative acyl-CoA dehydrogenase/0.440