Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
1dtnAPGMandelate racemase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1dtnAPGMandelate racemase/1.000
1mdlSMNMandelate racemase/0.577
1mdlRMNMandelate racemase/0.562
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.505
1yw7A41Methionine aminopeptidase 2/0.480
4xbjIN5Alanine racemase, biosynthetic/0.480
4xwtU5PRibonuclease J/0.479
3mesPT3Putative choline kinase/0.477
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.475
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.472
1z6tADPApoptotic protease-activating factor 1/0.470
3l0lHC3Nuclear receptor ROR-gamma/0.470
1ftlDNQGlutamate receptor 2/0.469
3jpuTY4Transcriptional activator protein LasR/0.469
4y7cNAPNADPH--cytochrome P450 reductase/0.469
2rds1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.468
3bj7COADiamine acetyltransferase 1/0.468
3gncQQQGlutaryl-CoA dehydrogenase/0.468
4h9tHL4Phosphotriesterase/0.468
1dduCB3Thymidylate synthase/0.466
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.466
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.466
4a99MIYTetX family tetracycline inactivation enzyme/0.466
3otwCOAPhosphopantetheine adenylyltransferase/0.464
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.463
1yw9A84Methionine aminopeptidase 2/0.463
2vn1FK5Peptidylprolyl isomerase/0.463
3tfn2CJDehydrosqualene synthase/0.463
4nieNBHNuclear receptor ROR-gamma/0.463
2xegCI9Glutamate carboxypeptidase 23.4.17.210.462
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.462
1lb9DNQGlutamate receptor 2/0.461
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
2e1zB4PPropionate kinase/0.461
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
4k36SAMAnaerobic sulfatase-maturating enzyme1.8.980.460
4mv1ADPBiotin carboxylase6.3.4.140.460
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.460
4yaw2AMNADPH--cytochrome P450 reductase/0.460
3ojiPYVAbscisic acid receptor PYL3/0.458
4fvz4KJNitric oxide synthase, brain1.14.13.390.458
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.457
1yqj6NPMitogen-activated protein kinase 14/0.456
2ea2F77Methionine aminopeptidase 2/0.456
3tfp03LDehydrosqualene synthase/0.456
4bis8HQLysine-specific demethylase 4A1.14.110.456
5bt9NAP3-oxoacyl-(Acyl-carrier-protein) reductase/0.456
1cq7PY5Aspartate aminotransferase2.6.1.10.455
3fr5I4AFatty acid-binding protein, adipocyte/0.455
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3c34KAIGlutamate receptor ionotropic, kainate 1/0.454
1r58AO5Methionine aminopeptidase 2/0.453
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
4b4w9L9Bifunctional protein FolD/0.453
1hb3SCVIsopenicillin N synthase1.21.3.10.452
2zbaZBATrichothecene 3-O-acetyltransferase/0.452
4i1nFOLDihydrofolate reductase1.5.1.30.452
1kzjCB3Thymidylate synthase/0.451
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.451
2ga2A19Methionine aminopeptidase 2/0.451
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.451
4bfsZVSPantothenate kinase2.7.1.330.451
1hb1OCVIsopenicillin N synthase1.21.3.10.450
2qqfA1RNAD-dependent protein deacetylase HST23.5.10.450
2vcmM11Isopenicillin N synthase1.21.3.10.450
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
4gd40WSLysine-specific demethylase 4A1.14.110.450
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.450
1mraAPGMandelate racemase/0.449
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
2ay3MPPAromatic-amino-acid aminotransferase2.6.1.570.449
2ea4F79Methionine aminopeptidase 2/0.449
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.449
2y67N21UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.449
3junAJDPhenazine biosynthesis protein A/B/0.449
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.449
3pm1ETHTH-type transcriptional regulator QacR/0.449
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.448
2q3eUPGUDP-glucose 6-dehydrogenase1.1.1.220.448
3h3t16HCollagen type IV alpha-3-binding protein/0.448
3nr4PYVAbscisic acid receptor PYL2/0.448
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.448
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
5kf9ACOPredicted acetyltransferase/0.448
1ix1BB2Peptide deformylase/0.447
1ove358Mitogen-activated protein kinase 14/0.447
2w6oOA3Biotin carboxylase6.3.4.140.447
3e6eDCSAlanine racemase/0.447
1b2lNDCAlcohol dehydrogenase1.1.1.10.446
1t1rIMB1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.446
2e0nSAHPrecorrin-2 C20-methyltransferase/0.446
3h3sH15Collagen type IV alpha-3-binding protein/0.446
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.446
4dyb0MHNucleoprotein/0.446
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.446
2geuCOKPantothenate kinase2.7.1.330.445
2v59LZKBiotin carboxylase6.3.4.140.445
3h3r14HCollagen type IV alpha-3-binding protein/0.445
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
5irnADPNucleotide binding oligomerization domain containing 2/0.445
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
3zkyWT4Isopenicillin N synthase1.21.3.10.444
4g090VDHistidinol dehydrogenase/0.444
4i6gFADCryptochrome-2/0.444
4jt91NSNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.444
4mv4ACPBiotin carboxylase6.3.4.140.444
1amoNAPNADPH--cytochrome P450 reductase/0.443
1ewyFADFerredoxin--NADP reductase1.18.1.20.443
1towCRZFatty acid-binding protein, adipocyte/0.443
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
4rvfTYDD-mycarose 3-C-methyltransferase/0.443
5kgjACOPredicted acetyltransferase/0.443
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
1oycFMNNADPH dehydrogenase 11.6.99.10.442
1txtCAAHMG-CoA synthase/0.442
1u1jC2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 12.1.1.140.442
2xejOKDGlutamate carboxypeptidase 23.4.17.210.442
3f03FMNPentaerythritol tetranitrate reductase/0.442
4awtFMNNADH:flavin oxidoreductase Sye1/0.442
4ixfIXFDihydrofolate reductase1.5.1.30.442
4mv8ACPBiotin carboxylase6.3.4.140.442
4y1bNAPAntE/0.442
1ao8MTXDihydrofolate reductase1.5.1.30.441
1fmjRTLRetinol dehydratase/0.441
1fmlRTLRetinol dehydratase/0.441
1mdrAPGMandelate racemase/0.441
1yw8A75Methionine aminopeptidase 2/0.441
2jf6S55Strictosidine-O-beta-D-glucosidase3.2.1.1050.441
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2wwjY28Lysine-specific demethylase 4A/0.441
3h03UBPGlutamate receptor 2/0.441
3n5wXFJNitric oxide synthase, brain1.14.13.390.441
4u9vACON-alpha-acetyltransferase 402.3.10.441
1kquBR4Phospholipase A2, membrane associated/0.440
1r5hAO2Methionine aminopeptidase 2/0.440
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2pamTYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.440
3c3eFO12-phospho-L-lactate transferase/0.440
3gc9B45Mitogen-activated protein kinase 112.7.11.240.440
3kzoAN0N-acetylornithine carbamoyltransferase2.1.3.90.440
4bfxZVXPantothenate kinase2.7.1.330.440
4cdmFO1Deoxyribodipyrimidine photolyase/0.440
4ead0NPThymidine phosphorylase2.4.2.40.440
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.440
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.440
4xnw2IDP2Y purinoceptor 1/0.440