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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
2xpc051UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.9

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2xpc051UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.91.000
2jfhLK1UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.636
2uuoLK3UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.634
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.630
1uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.620
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.607
2y67N21UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.536
2jfgUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.529
2y66N04UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.529
3p8iFMNPentaerythritol tetranitrate reductase/0.490
2wzySQXSoluble acetylcholine receptor/0.488
3gwfNAPCyclohexanone monooxygenase/0.486
3p74FMNPentaerythritol tetranitrate reductase/0.483
2uupLK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.481
1h63FMNPentaerythritol tetranitrate reductase/0.477
3h3t16HCollagen type IV alpha-3-binding protein/0.474
3f03FMNPentaerythritol tetranitrate reductase/0.468
1rzuADPGlycogen synthase 12.4.1.210.467
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.467
2xnvVU3Soluble acetylcholine receptor/0.467
1ygjRMCPyridoxal kinase2.7.1.350.465
2gv8NDPThiol-specific monooxygenase1.14.130.465
3zhuTD8Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.464
4kbyC2EStimulator of interferon genes protein/0.463
3eksCY9Actin-5C/0.462
3otwCOAPhosphopantetheine adenylyltransferase/0.462
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.462
3hgsFMN12-oxophytodienoate reductase 31.3.1.420.461
1enoNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.460
1q45FMN12-oxophytodienoate reductase 31.3.1.420.460
1xe65FPPlasmepsin-23.4.23.390.460
2g1n1IGRenin3.4.23.150.460
1h51FMNPentaerythritol tetranitrate reductase/0.459
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.459
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.459
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.459
1icpFMN12-oxophytodienoate reductase 11.3.1.420.458
1rneC60Renin3.4.23.150.458
1zgbA1EAcetylcholinesterase3.1.1.70.458
3p62FMNPentaerythritol tetranitrate reductase/0.458
3gf4UPGUDP-galactopyranose mutase5.4.99.90.457
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.456
1udaUFGUDP-glucose 4-epimerase5.1.3.20.456
2xysSY9Soluble acetylcholine receptor/0.456
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.456
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.456
3p8jFMNPentaerythritol tetranitrate reductase/0.456
2wqpWQPPolysialic acid capsule biosynthesis protein SiaC/0.455
3mj4URMUDP-galactopyranose mutase/0.455
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.455
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.453
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.453
2rhrEMOPutative ketoacyl reductase1.3.10.453
4xnw2IDP2Y purinoceptor 1/0.453
4cdmFO1Deoxyribodipyrimidine photolyase/0.452
4n4v2GYTankyrase-12.4.2.300.452
5a0112VO-glycosyltransferase/0.452
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
1toiHCIAspartate aminotransferase2.6.1.10.450
2xweAMFGlucosylceramidase3.2.1.450.450
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
1h50FMNPentaerythritol tetranitrate reductase/0.449
2zvbSAHPrecorrin-3 C17-methyltransferase/0.449
4a6rTA8Probable aminotransferase/0.449
1xuzMMNCapsule biosynthesis protein/0.448
2g226IGRenin3.4.23.150.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.448
4bfzZVZPantothenate kinase2.7.1.330.448
1fmlRTLRetinol dehydratase/0.447
2cmoM1LGlutamate receptor 2/0.447
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.447
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.447
2vn1FK5Peptidylprolyl isomerase/0.447
3b04OOPIsopentenyl-diphosphate delta-isomerase/0.447
3bl7DD1m7GpppX diphosphatase3.6.1.590.447
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.447
1bwlFMNNADPH dehydrogenase 11.6.99.10.446
1kquBR4Phospholipase A2, membrane associated/0.446
1m13HYFNuclear receptor subfamily 1 group I member 2/0.446
1u1gBBBUridine phosphorylase2.4.2.30.446
2g1y5IGRenin3.4.23.150.446
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.446
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.446
3hl0NADMaleylacetate reductase/0.446
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.446
4klaCHDFerrochelatase, mitochondrial4.99.1.10.446
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
2abbFMNPentaerythritol tetranitrate reductase/0.445
2q3oFMN12-oxophytodienoate reductase 31.3.1.420.445
3fr4F8AFatty acid-binding protein, adipocyte/0.445
4rphGDUUDP-galactopyranose mutase5.4.99.90.445
1lkeDOGBilin-binding protein/0.444
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.444
4p9dTMPDeoxycytidylate deaminase/0.444
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.444
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1x1bSAHC-20 methyltransferase/0.443
2i4qUA4Renin3.4.23.150.443
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3ekuCY9Actin-5C/0.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
4m83ERYOleandomycin glycosyltransferase2.4.10.443
2xlpFADPutative flavin-containing monooxygenase/0.442
3ndjJHZMethyltransferase/0.442
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.442
1yw7A41Methionine aminopeptidase 2/0.441
2g20L1ARenin3.4.23.150.441
2qimZEAClass 10 plant pathogenesis-related protein/0.441
2yj5ATPCopper-transporting ATPase/0.441
3csdEMOPutative ketoacyl reductase1.3.10.441
3dr7GPDGDP-perosamine synthase/0.441
3inrGDUUDP-galactopyranose mutase5.4.99.90.441
4bzbDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
4e2bFMNDehydrogenase/0.441
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4ihl1F514-3-3 protein zeta/delta/0.441
4kc4WS3Histo-blood group ABO system transferase/0.441
4mv1ADPBiotin carboxylase6.3.4.140.441
4xwtU5PRibonuclease J/0.441
1icqFMN12-oxophytodienoate reductase 11.3.1.420.440
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1rb3MTXDihydrofolate reductase1.5.1.30.440
1rftPXMPyridoxal kinase2.7.1.350.440
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.440
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.440
4zweDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440