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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
3sm0AEKQueuine tRNA-ribosyltransferase2.4.2.29

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3sm0AEKQueuine tRNA-ribosyltransferase2.4.2.291.000
4gh10WXQueuine tRNA-ribosyltransferase2.4.2.290.831
3ge7AFQQueuine tRNA-ribosyltransferase2.4.2.290.709
4gh30EVQueuine tRNA-ribosyltransferase2.4.2.290.687
4gg90WWQueuine tRNA-ribosyltransferase2.4.2.290.663
1q63AIQQueuine tRNA-ribosyltransferase2.4.2.290.661
4fps0UXQueuine tRNA-ribosyltransferase2.4.2.290.657
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.627
1y5vNE8Queuine tRNA-ribosyltransferase2.4.2.290.616
4gkt0O1Queuine tRNA-ribosyltransferase2.4.2.290.611
1y5xE89Queuine tRNA-ribosyltransferase2.4.2.290.602
1q65BHBQueuine tRNA-ribosyltransferase2.4.2.290.596
4giy0WYQueuine tRNA-ribosyltransferase2.4.2.290.575
4fr10V2Queuine tRNA-ribosyltransferase2.4.2.290.571
1q66KMBQueuine tRNA-ribosyltransferase2.4.2.290.549
1y5wNEZQueuine tRNA-ribosyltransferase2.4.2.290.542
2z1wBDIQueuine tRNA-ribosyltransferase2.4.2.290.541
3gc52MQQueuine tRNA-ribosyltransferase2.4.2.290.539
3gc4AAQQueuine tRNA-ribosyltransferase2.4.2.290.536
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.532
2z1xPRFQueuine tRNA-ribosyltransferase2.4.2.290.529
1ve3SAMUncharacterized protein/0.517
4fsa0V3Queuine tRNA-ribosyltransferase2.4.2.290.500
1q4wDQUQueuine tRNA-ribosyltransferase2.4.2.290.499
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.489
1n2vBDIQueuine tRNA-ribosyltransferase2.4.2.290.484
4gmgNAPYersiniabactin biosynthetic protein YbtU/0.480
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.478
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.476
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.476
1vbnYSATyrosine--tRNA ligase6.1.1.10.475
4q8pCKRQueuine tRNA-ribosyltransferase2.4.2.290.470
2wo7ASVIsopenicillin N synthase1.21.3.10.465
3bi6396Wee1-like protein kinase2.7.10.20.464
3cow52HPantothenate synthetase6.3.2.10.464
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.463
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.463
1zdgUPGGlycogenin-12.4.1.1860.462
2isc223Purine nucleoside phosphorylase, putative/0.462
2a4xBLMMitomycin-binding protein/0.461
2bbf344Queuine tRNA-ribosyltransferase2.4.2.290.461
4fex0TOAminoglycoside 3'-phosphotransferase AphA1-IAB/0.460
2qzrS79Queuine tRNA-ribosyltransferase2.4.2.290.458
2xauADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP433.6.4.130.458
3n87N873-dehydroquinate dehydratase4.2.1.100.458
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.458
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.458
3ts1TYATyrosine--tRNA ligase6.1.1.10.457
1r5yDQUQueuine tRNA-ribosyltransferase2.4.2.290.456
1t1sCBQ1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.455
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.454
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.452
3isjA8DPantothenate synthetase6.3.2.10.452
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.452
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.452
1ay0TPPTransketolase 12.2.1.10.451
1gaxVAAValine--tRNA ligase6.1.1.90.451
1kruIPTGalactoside O-acetyltransferase2.3.1.180.451
1ygkRRCPyridoxal kinase2.7.1.350.451
2vcmM11Isopenicillin N synthase1.21.3.10.450
4g95OAGDihydrofolate reductase1.5.1.30.450
3pdqKC6Lysine-specific demethylase 4A1.14.110.449
4at0FADPossible succinate dehydrogenase/0.449
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.448
1p0ePRFQueuine tRNA-ribosyltransferase2.4.2.290.448
3coz54HPantothenate synthetase6.3.2.10.448
4o4fATPKinase/0.448
4o4eATPKinase/0.447
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.446
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.446
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.10.446
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.446
3p9kSAHCaffeic acid O-methyltransferase/0.446
2z2w770Wee1-like protein kinase2.7.10.20.445
3nnz59WNitric oxide synthase, brain1.14.13.390.445
3oafOAGDihydrofolate reductase1.5.1.30.445
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.445
1x8b824Wee1-like protein kinase2.7.10.20.444
3n0tOPYDipeptidyl peptidase 23.4.14.20.444
3zkyWT4Isopenicillin N synthase1.21.3.10.444
1p44GEQEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
1u0wSTLChalcone synthase 22.3.1.740.443
1xmmM7Gm7GpppX diphosphatase3.6.1.590.443
4h3f10OBeta-secretase 13.4.23.460.443
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1lb9DNQGlutamate receptor 2/0.442
1zdwFLVPrenyltransferase/0.442
2cleF6FTryptophan synthase alpha chain/0.442
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.442
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.442
3udj092Beta-secretase 13.4.23.460.442
4b78KGGBeta-secretase 13.4.23.460.442
4gt8ADPSensor protein VraS2.7.13.30.442
1j7uANPAminoglycoside 3'-phosphotransferase2.7.1.950.441
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.441
4gg70J8Hepatocyte growth factor receptor2.7.10.10.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
3s6aANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.440
3ssoSAHMycinamicin VI 2''-O-methyltransferase/0.440
3sn6P0GBeta-2 adrenergic receptor/0.440