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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
1xliGLTXylose isomerase5.3.1.5

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1xliGLTXylose isomerase5.3.1.51.000
1xidASCXylose isomerase5.3.1.50.552
2gmuPDGPutative pyridoxamine 5-phosphate-dependent dehydrase/0.505
2xegCI9Glutamate carboxypeptidase 23.4.17.210.504
1diaL24C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.499
4lrhFOLFolate receptor alpha/0.498
4g090VDHistidinol dehydrogenase/0.496
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.494
1kw8BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.493
3lutNAPVoltage-gated potassium channel subunit beta-2/0.493
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.492
4fl0PLPAminotransferase ALD1, chloroplastic2.6.10.490
2gmsP0PPutative pyridoxamine 5-phosphate-dependent dehydrase/0.487
2bf4FMNNADPH--cytochrome P450 reductase/0.486
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.485
2y1x845Histone-arginine methyltransferase CARM1/0.485
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.485
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.484
2b5oFADFerredoxin--NADP reductase1.18.1.20.482
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.482
4lez1SYCyclic GMP-AMP synthase/0.482
1fmlRTLRetinol dehydratase/0.481
3ojgHL4Phosphotriesterase/0.480
4l4v1VYMajor histocompatibility complex class I-related gene protein/0.480
4xt8TMQPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.479
2c6c24IGlutamate carboxypeptidase 23.4.17.210.478
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.477
2q93B21Methionine aminopeptidase/0.473
1obnASVIsopenicillin N synthase1.21.3.10.472
1w6rGNTAcetylcholinesterase3.1.1.70.471
2cekN8TAcetylcholinesterase3.1.1.70.471
3e4aQIXInsulin-degrading enzyme3.4.24.560.471
3eufBAUUridine phosphorylase 1/0.471
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.471
4a7yNHFAldos-2-ulose dehydratase/0.471
1umaIN2Prothrombin3.4.21.50.469
4gaaBESLeukotriene A(4) hydrolase/0.469
1lnmDTXBilin-binding protein/0.468
2ea4F79Methionine aminopeptidase 2/0.468
2q96A18Methionine aminopeptidase/0.468
3dr4G4MGDP-perosamine synthase/0.468
3ojxFMNNADPH--cytochrome P450 reductase/0.468
1b2rFADFerredoxin--NADP reductase1.18.1.20.467
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.467
2pb1NFGGlucan 1,3-beta-glucosidase/0.467
1akbPPDAspartate aminotransferase, mitochondrial2.6.1.10.466
2fxuBIDActin, alpha skeletal muscle/0.466
4da50H7Choline kinase alpha2.7.1.320.466
1w4lGL8Acetylcholinesterase3.1.1.70.465
3l7gM44Xaa-Pro dipeptidase3.4.13.90.465
3m4p4ADAsparaginyl-tRNA synthetase, putative/0.465
3pkdY10Methionine aminopeptidase 2/0.465
2bn4FMNNADPH--cytochrome P450 reductase/0.464
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.464
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.464
1e62FADFerredoxin--NADP reductase1.18.1.20.463
2q94A04Methionine aminopeptidase/0.463
3iu9T07Methionine aminopeptidase 2/0.463
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.463
1amoFMNNADPH--cytochrome P450 reductase/0.462
2aovC2MHistamine N-methyltransferase2.1.1.80.462
2tplHPPTyrosine phenol-lyase4.1.99.20.462
2vn1FK5Peptidylprolyl isomerase/0.462
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.462
3fuhBESLeukotriene A-4 hydrolase3.3.2.60.462
4wljIK2Kynurenine--oxoglutarate transaminase 12.6.1.70.462
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.460
2zi53L1Deoxycytidine kinase2.7.1.740.460
3hr4FMNNitric oxide synthase, inducible1.14.13.390.460
3vjlW94Dipeptidyl peptidase 4/0.460
4drkI63Peptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.460
4e2yJHZMethyltransferase/0.460
4j7hTRHPCZA361.3/0.460
1o6qR17Squalene--hopene cyclase4.2.1.1290.459
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.459
2onfCOAUncharacterized protein/0.459
3cuiX4SExoglucanase/xylanase3.2.1.910.459
3ihzFK5Peptidylprolyl isomerase/0.459
4drn0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.459
4omaLCSMethionine gamma-lyase/0.459
4to3DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.459
2rd2QSIGlutamine--tRNA ligase6.1.1.180.458
4d6qPD2Lysine-specific demethylase 4D1.14.110.458
4isuIKMGlutamate receptor 2/0.458
4to4DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.458
1jf0CZHObelin/0.457
2v57PRLTetR family transcriptional regulator/0.457
2zi63D1Deoxycytidine kinase2.7.1.740.457
4d2cALA_PHEDi-or tripeptide:H+ symporter/0.457
4e32DWNMethyltransferase/0.457
4uugPXGBranched-chain amino acid aminotransferase, putative/0.457
1s0jMUSTrans-sialidase/0.456
1x8lOXRRetinol dehydratase/0.456
2gg8U15Methionine aminopeptidase/0.456
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.456
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.456
4x81MVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.456
1queFADFerredoxin--NADP reductase1.18.1.20.455
2j4dMHFCryptochrome DASH, chloroplastic/mitochondrial/0.455
3burTES3-oxo-5-beta-steroid 4-dehydrogenase/0.455
3qeoLLTDeoxycytidine kinase2.7.1.740.455
4xczT3QQdtf/0.455
1c23MPHMethionine aminopeptidase/0.454
1m2xMCOMetallo-beta-lactamase type 2/0.454
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.454
4b2gV1NUncharacterized protein/0.454
4iifCTSBeta-glucosidase 13.2.1.210.454
4rn615UProthrombin3.4.21.50.454
1e64FADFerredoxin--NADP reductase1.18.1.20.453
1kicNOSIAG-nucleoside hydrolase/0.453
3acy702Dehydrosqualene synthase/0.453
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.453
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.453
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.453
1toiHCIAspartate aminotransferase2.6.1.10.452
3lfzADPUncharacterized protein MJ1225/0.452
4a1oAMZBifunctional purine biosynthesis protein PurH2.1.2.30.452
4e2xTYDMethyltransferase/0.452
4to6TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.452
1enoNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.451
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1rxjBNIStreptavidin/0.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
2q92B23Methionine aminopeptidase/0.451
2v34CTN4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.451
2zg050UProthrombin3.4.21.50.451
3irhDTPHD domain protein/0.451
3iu8T03Methionine aminopeptidase 2/0.451
3qiyQI1Botulinum neurotoxin type A3.4.24.690.451
4j1h1HJBeta-secretase 13.4.23.460.451
1zgbA1EAcetylcholinesterase3.1.1.70.450
2a3cPNXEndochitinase B13.2.1.140.450
2ghtSER_PRO_THR_PRO_SEPCarboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 13.1.3.160.450
3fvuIACKynurenine--oxoglutarate transaminase 12.6.1.70.450
3k1wBFXRenin3.4.23.150.450
4a7zAY9Aldos-2-ulose dehydratase/0.450
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.450
4itxIN5Cystathionine beta-lyase MetC4.4.1.80.450
5ah5LSSLeucine--tRNA ligase/0.450
1fkgSB3Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.449
1p72THMThymidine kinase/0.449
1vrqFMNSubunit alpha of sarocosine oxidase/0.449
1vrqFMNSubunit beta of sarcosine oxidase/0.449
2gg0U11Methionine aminopeptidase/0.449
2oatPFMOrnithine aminotransferase, mitochondrial2.6.1.130.449
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.449
3n19FNRXenobiotic reductase/0.449
3pkaY02Methionine aminopeptidase 2/0.449
3vv8B02Beta-secretase 13.4.23.460.449
4nhyPD2Prolyl 3-hydroxylase OGFOD11.14.110.449
8catNDPCatalase1.11.1.60.449
1lb9DNQGlutamate receptor 2/0.448
1r5hAO2Methionine aminopeptidase 2/0.448
3d27W29Methionine aminopeptidase/0.448
3f8sPF2Dipeptidyl peptidase 4/0.448
3sfh1DIHistone deacetylase 83.5.1.980.448
3tfyMET_LEU_GLY_PRON-alpha-acetyltransferase 502.3.10.448
4nv1TYDFormyl transferase/0.448
1ahgTYR_PLPAspartate aminotransferase2.6.1.10.447
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.447
1blzACVIsopenicillin N synthase1.21.3.10.447
1isgAGSADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 23.2.2.60.447
1lkeDOGBilin-binding protein/0.447
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.447
3a5yKAAElongation factor P--(R)-beta-lysine ligase/0.447
3pkeY10Methionine aminopeptidase 2/0.447
3zm9QMQCholine kinase alpha2.7.1.320.447
4cb593GPolymerase basic protein 2/0.447
1a4wQWEProthrombin3.4.21.50.446
1e63FADFerredoxin--NADP reductase1.18.1.20.446
1eveE20Acetylcholinesterase3.1.1.70.446
1r5gAO1Methionine aminopeptidase 2/0.446
2ga2A19Methionine aminopeptidase 2/0.446
2jgbMGTEukaryotic translation initiation factor 4E type 2/0.446
2xysSY9Soluble acetylcholine receptor/0.446
3apyFADMethylenetetrahydrofolate reductase/0.446
3c35KAIGlutamate receptor ionotropic, kainate 1/0.446
3dr7GPDGDP-perosamine synthase/0.446
3gu3SAHMethyltransferase/0.446
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.446
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.446
1x2eATXProline iminopeptidase3.4.11.50.445
2w6pOA4Biotin carboxylase6.3.4.140.445
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.445
4gqkADPActin cross-linking toxin VgrG1/0.445
4j7gTRHPCZA361.3/0.445
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.445
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.444
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3fhxPLPPyridoxal kinase2.7.1.350.444
3ftxBESLeukotriene A-4 hydrolase3.3.2.60.444
3pkbY16Methionine aminopeptidase 2/0.444
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4f79P53Putative phospho-beta-glucosidase/0.444
4k97ATPCyclic GMP-AMP synthase/0.444
4r29SAMUncharacterized protein/0.444
1dpmEBPParathion hydrolase3.1.8.10.443
1og6NAPOxidoreductase YdhF10.443
1ut6A8NAcetylcholinesterase3.1.1.70.443
1ypkCCRProthrombin3.4.21.50.443
2v3oI26Prothrombin3.4.21.50.443
2x3jATPAcsD/0.443
4drp0MDPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.443
4frkDWDBeta-secretase 13.4.23.460.443
4iwnGEKCarboxy-S-adenosyl-L-methionine synthase/0.443
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
5d4vYGPUncharacterized protein MJ0489/0.443
1h42FADFerredoxin--NADP reductase1.18.1.20.442
1ihiIU5Aldo-keto reductase family 1 member C2/0.442
1lbbKAIGlutamate receptor 2/0.442
2xnvVU3Soluble acetylcholine receptor/0.442
2zfq45UProthrombin3.4.21.50.442
4mm729JNa(+):neurotransmitter symporter (Snf family)/0.442
4mqy2CWUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.442
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.441
1qgyFADFerredoxin--NADP reductase1.18.1.20.441
1yw8A75Methionine aminopeptidase 2/0.441
2evmFC2Methionine aminopeptidase/0.441
2geuCOKPantothenate kinase2.7.1.330.441
2xuhTZ4Acetylcholinesterase3.1.1.70.441
3c36KAIGlutamate receptor ionotropic, kainate 1/0.441
3e6eDCSAlanine racemase/0.441
3lzzGDPUncharacterized protein/0.441
3rthRTHBeta-secretase 13.4.23.460.441
3rviRVIBeta-secretase 13.4.23.460.441
3sfy3FYUncharacterized protein/0.441
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.441
4blcNDPCatalase1.11.1.60.441
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.441
4rvfTYDD-mycarose 3-C-methyltransferase/0.441
4xp4COCSodium-dependent dopamine transporter/0.441
4y7cFMNNADPH--cytochrome P450 reductase/0.441
5c8a5ADProbable transcriptional regulator/0.441
1g9dBABBotulinum neurotoxin type B3.4.24.690.440
1nc9IMIStreptavidin/0.440
1yw9A84Methionine aminopeptidase 2/0.440
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
2ix5CAAAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.440
3fpbATPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.440
3h3qH13Collagen type IV alpha-3-binding protein/0.440
3juqAJDPhenazine biosynthesis protein A/B/0.440
3mj4URMUDP-galactopyranose mutase/0.440
4araC56Acetylcholinesterase3.1.1.70.440
4dyb0MHNucleoprotein/0.440
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.440