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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
2o8bADPDNA mismatch repair protein Msh2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2o8bADPDNA mismatch repair protein Msh2/1.000
1wbbADPDNA mismatch repair protein MutS/0.525
2wo7ASVIsopenicillin N synthase1.21.3.10.503
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.488
1bk0ACVIsopenicillin N synthase1.21.3.10.487
1uhhCZPAequorin-2/0.483
1el4CTZObelin/0.481
2a9y26AAdenosine kinase2.7.1.200.480
1jf0CZHObelin/0.479
3b9oFMNAlkane monoxygenase/0.479
4oztP1AEcdysone receptor, putative/0.478
1h60STRPentaerythritol tetranitrate reductase/0.477
3q9bB3NAcetylpolyamine amidohydrolase/0.477
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.474
1qv0CZHObelin/0.473
4esoNAPPutative oxidoreductase/0.473
4rh10TTSpore photoproduct lyase/0.473
1j9zFADNADPH--cytochrome P450 reductase/0.472
2bu9HFVIsopenicillin N synthase1.21.3.10.472
1ej3CZHAequorin-2/0.471
1u0wSTLChalcone synthase 22.3.1.740.470
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.470
4n3l2FNProthrombin3.4.21.50.470
2bvs2CEProthrombin3.4.21.50.469
2zevIPEGeranylgeranyl pyrophosphate synthase/0.469
4ehyADPTetraacyldisaccharide 4'-kinase/0.469
2ejzSAHDiphthine synthase/0.467
3ho9N3A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.467
2gevCOKPantothenate kinase2.7.1.330.465
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.465
2gjnFMNNitronate monooxygenase1.13.12.160.464
2vcmM11Isopenicillin N synthase1.21.3.10.464
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
1enoNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.463
2e17SAHDiphthine synthase/0.463
2rehFADNitroalkane oxidase1.7.3.10.463
3keqNADRedox-sensing transcriptional repressor Rex/0.463
3fazNOSPurine nucleoside phosphorylase/0.462
1e66HUXAcetylcholinesterase3.1.1.70.461
2rlcCHDCholoylglycine hydrolase3.5.1.240.461
3otwCOAPhosphopantetheine adenylyltransferase/0.461
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.460
3iktNADRedox-sensing transcriptional repressor Rex/0.460
7stdCRPScytalone dehydratase4.2.1.940.460
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.459
1w1wAGSStructural maintenance of chromosomes protein 1/0.459
2e0nSAHPrecorrin-2 C20-methyltransferase/0.459
2iviACWIsopenicillin N synthase1.21.3.10.459
2jb4A14Isopenicillin N synthase1.21.3.10.459
2pckSAHDiphthine synthase/0.459
2pswCOAN-alpha-acetyltransferase 50/0.459
2vbpVB1Isopenicillin N synthase1.21.3.10.459
3h3qH13Collagen type IV alpha-3-binding protein/0.459
4s1iPLPPyridoxal kinase, putative/0.459
4v0s2HN3-dehydroquinate dehydratase4.2.1.100.459
5stdUNNScytalone dehydratase4.2.1.940.459
1h2bNAJNAD-dependent alcohol dehydrogenase/0.458
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.458
1zgv501Prothrombin3.4.21.50.458
2owfSAHDiphthine synthase/0.458
4bb3KKAIsopenicillin N synthase1.21.3.10.458
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.457
1pwuGM6Lethal factor3.4.24.830.457
2gjlFMNNitronate monooxygenase1.13.12.160.457
3br3ETHTH-type transcriptional regulator QacR/0.457
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.457
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3r5yF42Uncharacterized protein/0.457
1qiqACCIsopenicillin N synthase1.21.3.10.456
1towCRZFatty acid-binding protein, adipocyte/0.456
1uhjCZBAequorin-2/0.456
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.456
2eldSAHDiphthine synthase/0.456
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.456
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.456
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.456
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.456
4mk728OGenome polyprotein2.7.7.480.456
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.455
2zgb21UProthrombin3.4.21.50.455
4ho6UTPGlucose-1-phosphate thymidylyltransferase/0.455
1dljUGAUDP-glucose 6-dehydrogenase/0.454
2xlpFADPutative flavin-containing monooxygenase/0.454
3fhxPLPPyridoxal kinase2.7.1.350.454
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.454
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.454
3nmpPYVAbscisic acid receptor PYL2/0.454
3wqmB29Diterpene synthase3.1.7.80.454
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.454
1d6w00RProthrombin3.4.21.50.453
1w6jR71Lanosterol synthase5.4.99.70.453
1ygjRMCPyridoxal kinase2.7.1.350.453
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.453
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
4fhd0TTSpore photoproduct lyase/0.453
1h66RH1NAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.452
3bi2FADPolyamine oxidase FMS1/0.452
3hucG97Mitogen-activated protein kinase 14/0.452
3p0fBAUUridine phosphorylase 22.4.2.30.452
4bdrKAIGlutamate receptor ionotropic, kainate 2/0.452
4twnB96Ephrin type-A receptor 32.7.10.10.452
4xq6FMNDihydroorotate dehydrogenase (quinone)/0.452
1blzACVIsopenicillin N synthase1.21.3.10.451
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.451
2vbdV10Isopenicillin N synthase1.21.3.10.451
3bi6396Wee1-like protein kinase2.7.10.20.451
3ddw055Glycogen phosphorylase, liver form2.4.1.10.451
3l7gM44Xaa-Pro dipeptidase3.4.13.90.451
3zkyWT4Isopenicillin N synthase1.21.3.10.451
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.451
1t57FMNConserved protein/0.450
1zq5E04Aldo-keto reductase family 1 member C3/0.450
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.450
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3eq02TSProthrombin3.4.21.50.450
3hwxTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.450
3stdMQ0Scytalone dehydratase4.2.1.940.450
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.449
2pk3GDDGDP-6-deoxy-D-mannose reductase/0.449
2ptfFMNUncharacterized protein MTH_863/0.449
2zfq45UProthrombin3.4.21.50.449
3gncQQQGlutaryl-CoA dehydrogenase/0.449
4biwANPSensor histidine kinase CpxA/0.449
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.449
1c4yIH3Prothrombin3.4.21.50.448
1hb1OCVIsopenicillin N synthase1.21.3.10.448
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.448
2on6IMHPurine nucleoside phosphorylase2.4.2.10.448
2z6rSAHDiphthine synthase/0.448
3mjrAC2Deoxycytidine kinase2.7.1.740.448
3qgi33FGenome polyprotein2.7.7.480.448
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
4bmoFMNProtein NrdI/0.448
4n1fCZHObelin/0.448
6stdMS2Scytalone dehydratase4.2.1.940.448
1cneFADNitrate reductase [NADH]1.7.1.10.447
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.447
1umaIN2Prothrombin3.4.21.50.447
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2zi224UProthrombin3.4.21.50.447
3t94MTAS-methyl-5'-thioadenosine phosphorylase/0.447
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.447
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.447
4y1bNAPAntE/0.447
1hb3SCVIsopenicillin N synthase1.21.3.10.446
1t4v14AProthrombin3.4.21.50.446
2jl1NAPTriphenylmethane reductase/0.446
3btjDEQHTH-type transcriptional regulator QacR/0.446
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.446
4bfzZVZPantothenate kinase2.7.1.330.446
4g2gTDHMycocyclosin synthase1.14.21.90.446
4g47TZFMycocyclosin synthase1.14.21.90.446
4zqcF6FTryptophan synthase alpha chain/0.446
1kziTHGThymidylate synthase/0.445
1n3sGTPGTP cyclohydrolase 13.5.4.160.445
1stdBFSScytalone dehydratase4.2.1.940.445
1tj0FADBifunctional protein PutA1.5.5.20.445
1w19T4P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
2bjsACVIsopenicillin N synthase1.21.3.10.445
2pb4SAHDiphthine synthase/0.445
2pcaSAHDiphthine synthase/0.445
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.445
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.445
3pftFMNFlavin reductase/0.445
3sl2ATPSensor histidine kinase WalK/0.445
3znqSS8D-amino-acid oxidase1.4.3.30.445
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.445
4ax9N5NProthrombin3.4.21.50.445
4fhf0TTSpore photoproduct lyase/0.445
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.445
1dnaCB3Thymidylate synthase/0.444
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
1vceSAHDiphthine synthase/0.444
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.444
2zhf49UProthrombin3.4.21.50.444
3fsjD7KBenzoylformate decarboxylase4.1.1.70.444
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.444
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.444
3t3iGPWGlycogen phosphorylase, muscle form2.4.1.10.444
3uweVJJAldo-keto reductase family 1 member C3/0.444
3v0n4GWHisto-blood group ABO system transferase/0.444
3v0p4GWHisto-blood group ABO system transferase/0.444
4b6r3DQ3-dehydroquinate dehydratase4.2.1.100.444
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.444
4do30LAFatty-acid amide hydrolase 13.5.1.990.444
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.444
4k9oTPPBenzoylformate decarboxylase4.1.1.70.444
4xz3COAAcyl-CoA synthetase (NDP forming)/0.444
4yx6FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.444
1g7vPAI2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.443
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2e07SAHDiphthine synthase/0.443
2vd0D27Hematopoietic prostaglandin D synthase/0.443
2zdv37UProthrombin3.4.21.50.443
2zfp19UProthrombin3.4.21.50.443
3h2lYAKGenome polyprotein2.7.7.480.443
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4j7hTRHPCZA361.3/0.443
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.443
1qoqIGPTryptophan synthase alpha chain/0.442
1z71L17Prothrombin3.4.21.50.442
2a9z26AAdenosine kinase2.7.1.200.442
2c9bPUG6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2ed3SAHDiphthine synthase/0.442
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.442
2z3uCRRCytochrome P450/0.442
3akn11DFatty acid-binding protein, intestinal/0.442
3bi5FADPolyamine oxidase FMS1/0.442
3c1kT15Prothrombin3.4.21.50.442
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.442
3r43ID8Aldo-keto reductase family 1 member C3/0.442
4fam0SZAldo-keto reductase family 1 member C3/0.442
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.442
4u0mGTPCyclic GMP-AMP synthase/0.442
5dhgDGVNociceptin receptor/0.442
1d9i00PProthrombin3.4.21.50.441
1gpnHUBAcetylcholinesterase3.1.1.70.441
1p33MTXPteridine reductase 11.5.1.330.441
2e4nSAHDiphthine synthase/0.441
2hxzH7JCathepsin S3.4.22.270.441
2r0pK2CPutative FAD-monooxygenase/0.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3eksCY9Actin-5C/0.441
3fr5I4AFatty acid-binding protein, adipocyte/0.441
4y9lFADAcyl-CoA dehydrogenase family member 11/0.441
5c1gGDUHisto-blood group ABO system transferase/0.441
1d3pBT3Prothrombin3.4.21.50.440
1ez0NAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.440
1fmjRTLRetinol dehydratase/0.440
1jf2CZHObelin/0.440
1knrFADL-aspartate oxidase1.4.3.160.440
1tkcM6TTransketolase 12.2.1.10.440
1typFADTrypanothione reductase1.8.1.120.440
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.440
2g8yNADHydroxycarboxylate dehydrogenase B/0.440
2nx3PEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.440
2pksG44Prothrombin3.4.21.50.440
3ce0P34Poly [ADP-ribose] polymerase 32.4.2.300.440
3fhxPXLPyridoxal kinase2.7.1.350.440
3qeoLLTDeoxycytidine kinase2.7.1.740.440
3rsv3RSBeta-secretase 13.4.23.460.440
4blcNDPCatalase1.11.1.60.440
4l5aTBNS-methyl-5'-thioadenosine phosphorylase/0.440
4nqgCZHMitrocomin/0.440
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.440