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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
2x1lADNMethionine--tRNA ligase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2x1lADNMethionine--tRNA ligase/1.000
2ct8MSPMethionine--tRNA ligase6.1.1.100.503
1pg0MODMethionine--tRNA ligase6.1.1.100.501
1pfyMSPMethionine--tRNA ligase6.1.1.100.496
1qu2MRCIsoleucine--tRNA ligase6.1.1.50.488
1ffyMRCIsoleucine--tRNA ligase6.1.1.50.485
3c35KAIGlutamate receptor ionotropic, kainate 1/0.484
4f1yCNIGlutamate receptor 3/0.476
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.473
2g1a5HGClass B acid phosphatase3.1.3.20.471
3b7dCNIGlutamate receptor 2/0.468
3arvSAUChitinase A/0.466
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.463
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
4gh10WXQueuine tRNA-ribosyltransferase2.4.2.290.461
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.460
1pg2ADNMethionine--tRNA ligase6.1.1.100.460
1ry8RUTAldo-keto reductase family 1 member C3/0.459
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.459
3c36KAIGlutamate receptor ionotropic, kainate 1/0.459
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.459
1fw0KAIGlutamate receptor 2/0.458
4n3l2FNProthrombin3.4.21.50.458
1ppjANYCytochrome b/0.457
3dzjNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.456
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.456
4h0xNADIota toxin component Ia/0.456
2rcwAAIPoly [ADP-ribose] polymerase 12.4.2.300.455
3ce0P34Poly [ADP-ribose] polymerase 32.4.2.300.455
4m2bUPGUDP-glucose pyrophosphorylase/0.455
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.455
2b82ADNClass B acid phosphatase3.1.3.20.454
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.454
2b8jADNClass B acid phosphatase3.1.3.20.453
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.452
3rm8RM8Acidic mammalian chitinase3.2.1.140.452
1q63AIQQueuine tRNA-ribosyltransferase2.4.2.290.451
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.451
3cr0809Wee1-like protein kinase2.7.10.20.451
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.450
4a86H35Major pollen allergen Bet v 1-A/0.449
4m4821BSodium-dependent dopamine transporter/0.449
4xp4COCSodium-dependent dopamine transporter/0.449
1w19T4P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
1oc1ASVIsopenicillin N synthase1.21.3.10.447
2rd678PPoly [ADP-ribose] polymerase 12.4.2.300.447
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
2q0gUPUPoly(A) polymerase, putative/0.446
3rtnRTNBeta-secretase 13.4.23.460.446
4psbGA3Cytokinin-specific binding protein/0.446
2r2mI50Prothrombin3.4.21.50.445
3c27DKKProthrombin3.4.21.50.445
1lbbKAIGlutamate receptor 2/0.444
2bn4FADNADPH--cytochrome P450 reductase/0.444
3rsv3RSBeta-secretase 13.4.23.460.444
3rviRVIBeta-secretase 13.4.23.460.443
1pqc444Oxysterols receptor LXR-beta/0.442
1zq5E04Aldo-keto reductase family 1 member C3/0.442
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.442
4yao2AMNADPH--cytochrome P450 reductase/0.442
3qeoLLTDeoxycytidine kinase2.7.1.740.441