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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
3biv11UProthrombin3.4.21.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3biv11UProthrombin3.4.21.51.000
2znk31UProthrombin3.4.21.50.881
2zi224UProthrombin3.4.21.50.856
2zdv37UProthrombin3.4.21.50.852
2zg050UProthrombin3.4.21.50.841
2zda32UProthrombin3.4.21.50.838
2zgx29UProthrombin3.4.21.50.813
3biu10UProthrombin3.4.21.50.803
2zc922UProthrombin3.4.21.50.791
2ziq26UProthrombin3.4.21.50.790
2zhf49UProthrombin3.4.21.50.784
2zfq45UProthrombin3.4.21.50.781
2zff53UProthrombin3.4.21.50.777
2zhe13UProthrombin3.4.21.50.751
3dhk23UProthrombin3.4.21.50.750
4ax9N5NProthrombin3.4.21.50.744
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.735
3dux64UProthrombin3.4.21.50.721
3eq02TSProthrombin3.4.21.50.721
2zhq27UProthrombin3.4.21.50.718
2zgb21UProthrombin3.4.21.50.706
4bamMM9Prothrombin3.4.21.50.694
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.680
1ypgUIRProthrombin3.4.21.50.679
1mueCDDProthrombin3.4.21.50.676
1d6w00RProthrombin3.4.21.50.668
2zf051UProthrombin3.4.21.50.667
2zfp19UProthrombin3.4.21.50.664
2r2mI50Prothrombin3.4.21.50.655
3f6891UProthrombin3.4.21.50.655
1zrb062Prothrombin3.4.21.50.654
1ypkCCRProthrombin3.4.21.50.648
2jh5895Prothrombin3.4.21.50.647
1d4pBPPProthrombin3.4.21.50.645
1k21IGNProthrombin3.4.21.50.642
3egkM18Prothrombin3.4.21.50.642
4bakM67Prothrombin3.4.21.50.642
1afeALZProthrombin3.4.21.50.640
2anmCDOProthrombin3.4.21.50.640
1ta6177Prothrombin3.4.21.50.639
2bvs2CEProthrombin3.4.21.50.636
1o0d163Prothrombin3.4.21.50.632
3qwc98PProthrombin3.4.21.50.632
1ae8AZLProthrombin3.4.21.50.630
1t4u81AProthrombin3.4.21.50.628
2v3oI26Prothrombin3.4.21.50.628
1z71L17Prothrombin3.4.21.50.626
1mu8CDBProthrombin3.4.21.50.624
1ypeUIPProthrombin3.4.21.50.624
3c1kT15Prothrombin3.4.21.50.623
1c4uIH1Prothrombin3.4.21.50.620
1sb1165Prothrombin3.4.21.50.620
1ta2176Prothrombin3.4.21.50.617
4lxb7R9Prothrombin3.4.21.50.615
1xm1GAHProthrombin3.4.21.50.614
3qto10PProthrombin3.4.21.50.611
1mu6CDAProthrombin3.4.21.50.610
1ypjUIBProthrombin3.4.21.50.610
2zhw12UProthrombin3.4.21.50.607
4baqM4ZProthrombin3.4.21.50.607
1d3dBZTProthrombin3.4.21.50.606
3p1799PProthrombin3.4.21.50.602
2jh0701Prothrombin3.4.21.50.601
1d9i00PProthrombin3.4.21.50.597
3c27DKKProthrombin3.4.21.50.596
1jwtBLIProthrombin3.4.21.50.594
1ypmRA4Prothrombin3.4.21.50.594
2gdeSN3Prothrombin3.4.21.50.586
1vzqSHYProthrombin3.4.21.50.583
4ayy9MXProthrombin3.4.21.50.579
4bahMELProthrombin3.4.21.50.579
3utu1TSProthrombin3.4.21.50.578
2cf9348Prothrombin3.4.21.50.577
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.576
1oytFSNProthrombin3.4.21.50.575
4hfp15UProthrombin3.4.21.50.572
2bdyUNBProthrombin3.4.21.50.571
1c4yIH3Prothrombin3.4.21.50.569
2cn0F25Prothrombin3.4.21.50.569
2uuj896Prothrombin3.4.21.50.569
2a2xNA9Prothrombin3.4.21.50.567
2pksG44Prothrombin3.4.21.50.567
1uvsI11Prothrombin3.4.21.50.566
2v3hI25Prothrombin3.4.21.50.566
1nzq162Prothrombin3.4.21.50.565
3qtv06PProthrombin3.4.21.50.565
4n3l2FNProthrombin3.4.21.50.565
1ghv120Prothrombin3.4.21.50.561
1nm6L86Prothrombin3.4.21.50.560
4baoMVFProthrombin3.4.21.50.560
2cf8ESHProthrombin3.4.21.50.559
1c4vIH2Prothrombin3.4.21.50.558
4az29MUProthrombin3.4.21.50.557
4e7r0NWProthrombin3.4.21.50.556
4loy6XSProthrombin3.4.21.50.556
1d3pBT3Prothrombin3.4.21.50.554
4rn615UProthrombin3.4.21.50.547
1c5nESIProthrombin3.4.21.50.546
1gj4132Prothrombin3.4.21.50.539
1k22MELProthrombin3.4.21.50.538
1gj5130Prothrombin3.4.21.50.537
2bxtC2DProthrombin3.4.21.50.532
1ktsC24Prothrombin3.4.21.50.528
1bcuPRLProthrombin3.4.21.50.523
1yplRA8Prothrombin3.4.21.50.522
1a4wQWEProthrombin3.4.21.50.519
1w7gMIUProthrombin3.4.21.50.516
4ayv9MQProthrombin3.4.21.50.514
1o2g696Prothrombin3.4.21.50.513
4b1jA1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.509
5irnADPNucleotide binding oligomerization domain containing 2/0.498
1riwOSCProthrombin3.4.21.50.496
1o5gCR9Prothrombin3.4.21.50.491
2po7CHDFerrochelatase, mitochondrial4.99.1.10.489
2qimZEAClass 10 plant pathogenesis-related protein/0.489
1zsk421Coagulation factor XI3.4.21.270.487
5cmx0G6Prothrombin3.4.21.50.487
1wqvPSMCoagulation factor VII3.4.21.210.485
2rqfJH3Hemolymph juvenile hormone binding protein/0.480
2zp0PI0Coagulation factor VII3.4.21.210.477
1b2lNDCAlcohol dehydrogenase1.1.1.10.474
1c1uBAIProthrombin3.4.21.50.474
2cv2GSUGlutamate--tRNA ligase6.1.1.170.474
2g247IGRenin3.4.23.150.472
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.472
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.472
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.471
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.471
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.470
1oc1ASVIsopenicillin N synthase1.21.3.10.470
2j83BATUlilysin3.4.240.470
4fuf8UPUrokinase-type plasminogen activator3.4.21.730.470
2nr4FMNConserved protein/0.468
4fue7UPUrokinase-type plasminogen activator3.4.21.730.468
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.467
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.465
5f8fSFGPossible transcriptional regulatory protein/0.465
1obnASVIsopenicillin N synthase1.21.3.10.464
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.464
2pg0FADAcyl-CoA dehydrogenase/0.464
2rlcCHDCholoylglycine hydrolase3.5.1.240.463
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
4a83DXCMajor pollen allergen Bet v 1-A/0.463
4d03NAPPhenylacetone monooxygenase1.14.13.920.463
4i4z2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.463
4q71FADBifunctional protein PutA/0.463
2y60M8FIsopenicillin N synthase1.21.3.10.462
4lzwTHMUridine phosphorylase/0.462
5ejaTD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.462
1hb3SCVIsopenicillin N synthase1.21.3.10.461
1hkuNADC-terminal-binding protein 11.1.10.461
2xb9XNW3-dehydroquinate dehydratase4.2.1.100.461
2xuoTZ4Acetylcholinesterase3.1.1.70.461
4m0f1YKAcetylcholinesterase3.1.1.70.461
1c1wBAHProthrombin3.4.21.50.460
3fhxPXLPyridoxal kinase2.7.1.350.460
3fpdSAHHistone-lysine N-methyltransferase EHMT1/0.460
3oafOAGDihydrofolate reductase1.5.1.30.460
4a862ANMajor pollen allergen Bet v 1-A/0.460
4mlp2CXCryptochrome-2/0.460
4yjdFADD-amino-acid oxidase1.4.3.30.460
4bb3KKAIsopenicillin N synthase1.21.3.10.459
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.459
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.459
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.458
2g004QCCoagulation factor X3.4.21.60.458
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.458
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.458
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.458
2gv8NDPThiol-specific monooxygenase1.14.130.457
3mo0SAHHistone-lysine N-methyltransferase EHMT1/0.457
3swcSAHHistone-lysine N-methyltransferase EHMT1/0.457
1f20FADNitric oxide synthase, brain1.14.13.390.456
2abaSTRPentaerythritol tetranitrate reductase/0.456
2hxzH7JCathepsin S3.4.22.270.456
3ic9FADPutative dihydrolipoamide dehydrogenase/0.456
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3s7dLEU_SER_LYS_LYS_MLZN-lysine methyltransferase SMYD2/0.456
3wqmB29Diterpene synthase3.1.7.80.456
4ejmNAPPutative zinc-binding dehydrogenase/0.456
3zoiM2WIsopenicillin N synthase1.21.3.10.455
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
4ey6GNTAcetylcholinesterase3.1.1.70.455
4g95OAGDihydrofolate reductase1.5.1.30.455
1pqc444Oxysterols receptor LXR-beta/0.454
1rkwPNTHTH-type transcriptional regulator QacR/0.454
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.454
2iviACWIsopenicillin N synthase1.21.3.10.454
2p2mPRXAcetyl-coenzyme A synthetase/0.454
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3ai0PNWBeta-glucosidase/0.454
1owe675Urokinase-type plasminogen activator3.4.21.730.453
2c4fGILCoagulation factor VII3.4.21.210.453
2dxdANPNucleoside diphosphate kinase2.7.4.60.453
2j14GNIPeroxisome proliferator-activated receptor delta/0.453
2nq8ZIDEnoyl-ACP reductase/0.453
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.453
2y6fM9FIsopenicillin N synthase1.21.3.10.453
3g70A5TRenin3.4.23.150.453
3hu1AGSTransitional endoplasmic reticulum ATPase3.6.4.60.453
3wagTYDGlycosyltransferase/0.453
4m5pFMNNADPH dehydrogenase/0.453
4xbjIN5Alanine racemase, biosynthetic/0.453
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.453
1sl3170Prothrombin3.4.21.50.452
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.452
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.452
3k1wBFXRenin3.4.23.150.452
3sp9IL2Peroxisome proliferator-activated receptor delta/0.452
4y1bNAPAntE/0.452
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1owk303Urokinase-type plasminogen activator3.4.21.730.451
1p0hCOAMycothiol acetyltransferase2.3.1.1890.451
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.451
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.451
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.451
3h3qH13Collagen type IV alpha-3-binding protein/0.451
3v4aPK1Androgen receptor/0.451
2bu9HFVIsopenicillin N synthase1.21.3.10.450
3fp0FP015-O-acetyltransferase/0.450
3h3t16HCollagen type IV alpha-3-binding protein/0.450
3pm1ETHTH-type transcriptional regulator QacR/0.450
3vilSA0Beta-glucosidase/0.450
4b1rITCTetracycline repressor protein class D/0.450
1kheGCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.449
1ma0NADAlcohol dehydrogenase class-31.1.1.10.449
1oklMNSCarbonic anhydrase 24.2.1.10.449
1q84TZ4Acetylcholinesterase3.1.1.70.449
2g8yNADHydroxycarboxylate dehydrogenase B/0.449
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.449
2xugTZ4Acetylcholinesterase3.1.1.70.449
3e2sFADBifunctional protein PutA1.5.5.20.449
4fuiUI3Urokinase-type plasminogen activator3.4.21.730.449
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.449
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.449
5jhnSAMHistone-lysine N-methyltransferase EHMT2/0.449
1icvFMNOxygen-insensitive NAD(P)H nitroreductase/0.448
3c36KAIGlutamate receptor ionotropic, kainate 1/0.448
3o0iP54Heat shock protein HSP 90-alpha/0.448
3po6DT9Carbonic anhydrase 24.2.1.10.448
5hs1VORLanosterol 14-alpha demethylase/0.448
1khbGCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.447
1nhkCMPNucleoside diphosphate kinase2.7.4.60.447
1rz1NADPhenol 2-hydroxylase component B/0.447
1rzuADPGlycogen synthase 12.4.1.210.447
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.447
4a87NARMajor pollen allergen Bet v 1-A/0.447
4eb7PLPCysteine desulfurase IscS 2/0.447
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.447
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.447
4uugPXGBranched-chain amino acid aminotransferase, putative/0.447
1hb1OCVIsopenicillin N synthase1.21.3.10.446
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.446
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.446
1tsxUMPThymidylate synthase/0.446
1uymPU3Heat shock protein HSP 90-beta/0.446
1vbiNADMalate/L-lactate dehydrogenase family protein/0.446
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2fe4GDPRas-related protein Rab-6B/0.446
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.446
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.446
2vyqFADFerredoxin--NADP reductase1.18.1.20.446
2ym1NAPPhenylacetone monooxygenase1.14.13.920.446
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3qviK95HAP protein/0.446
4alxIZNAcetylcholine-binding protein/0.446
5f54TMPSingle-stranded-DNA-specific exonuclease/0.446
1culFOKAdenylate cyclase type 2/0.445
1culFOKAdenylate cyclase type 5/0.445
1x1rGDPRas-related protein M-Ras/0.445
2bsxNOSPurine nucleoside phosphorylase/0.445
2xuiTZ5Acetylcholinesterase3.1.1.70.445
2xujTZ5Acetylcholinesterase3.1.1.70.445
2y5hY5HCoagulation factor X3.4.21.60.445
2zshGA3Gibberellin receptor GID1A30.445
3gwfNAPCyclohexanone monooxygenase/0.445
3h4vNAPPteridine reductase 11.5.1.330.445
3hl0NADMaleylacetate reductase/0.445
3ho9N3A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.445
3phiNDPShikimate dehydrogenase (NADP(+))/0.445
3vev0H4Glucokinase2.7.1.20.445
4bekXK0Beta-secretase 13.4.23.460.445
4kos4KOUncharacterized protein/0.445
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.445
4nieNBHNuclear receptor ROR-gamma/0.445
4xbfFADLysine-specific histone demethylase 1A10.445
1nyxDRFPeroxisome proliferator-activated receptor gamma/0.444
1ozvSAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.444
2g1s4IGRenin3.4.23.150.444
2ptfFMNUncharacterized protein MTH_863/0.444
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.444
4bfxZVXPantothenate kinase2.7.1.330.444
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.444
4jln18VDeoxycytidine kinase2.7.1.740.444
4q0kGA3Phytohormone-binding protein/0.444
5stdUNNScytalone dehydratase4.2.1.940.444
1rszDIHPurine nucleoside phosphorylase2.4.2.10.443
1rxjBNIStreptavidin/0.443
1wliFMNFMN-binding protein/0.443
3zhoFMNNAD(P)H dehydrogenase (quinone)/0.443
4b1e6T6Beta-secretase 13.4.23.460.443
4g2rH1LProbable propionyl-CoA carboxylase beta chain 66.4.1.30.443
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4i8vBHFCytochrome P450 1A11.14.14.10.443
1bk0ACVIsopenicillin N synthase1.21.3.10.442
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.442
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.442
1o1t2NHProtein farnesyltransferase subunit beta2.5.1.580.442
1p0pBCHCholinesterase3.1.1.80.442
1w1wAGSStructural maintenance of chromosomes protein 1/0.442
1zdwFLVPrenyltransferase/0.442
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.442
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.442
2pswCOAN-alpha-acetyltransferase 50/0.442
2vbdV10Isopenicillin N synthase1.21.3.10.442
2wu4HBPAcetylcholinesterase3.1.1.70.442
2ykjYKJHeat shock protein HSP 90-alpha/0.442
2yltFADPhenylacetone monooxygenase1.14.13.920.442
3g11P9C3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.442
3nsh957Beta-secretase 13.4.23.460.442
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4i0i957Beta-secretase 13.4.23.460.442
1nfyRTRCoagulation factor X3.4.21.60.441
1puaCOAHAT A1/0.441
1qtiGNTAcetylcholinesterase3.1.1.70.441
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.441
2cndFADNitrate reductase [NADH]1.7.1.10.441
2xvfFADPutative flavin-containing monooxygenase/0.441
3adaNADSubunit alpha of sarocosine oxidase/0.441
3b4fTUOCarbonic anhydrase 24.2.1.10.441
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3f3y4OABile salt sulfotransferase2.8.2.140.441
4bubADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase/0.441
4eqkMGTPolymerase basic protein 2/0.441
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.441
4fub4UPUrokinase-type plasminogen activator3.4.21.730.441
4i421HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.441
4uthFMNXenobiotic reductase/0.441
1c7oPPGHemolysin/0.440
1lqdCMICoagulation factor X3.4.21.60.440
1uxkNADMalate dehydrogenase/0.440
1x1cSAHC-20 methyltransferase/0.440
1zbdGTPRas-related protein Rab-3A/0.440
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.440
2qw034Z4-chlorobenzoyl CoA ligase/0.440
2x96RX3Angiotensin-converting enzyme3.4.15.10.440
2xluNA7Putative flavin-containing monooxygenase/0.440
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
2zbaZBATrichothecene 3-O-acetyltransferase/0.440
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.440
3qgf46FGenome polyprotein2.7.7.480.440
3tg4SAMN-lysine methyltransferase SMYD2/0.440
3wv9FEGHmd co-occurring protein HcgE/0.440
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.440
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.440
4j33FADKynurenine 3-monooxygenase/0.440
4jtqFLPAldo-keto reductase family 1 member C2/0.440
4oztP1AEcdysone receptor, putative/0.440