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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1xjeTTPVitamin B12-dependent ribonucleotide reductase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1xjeTTPVitamin B12-dependent ribonucleotide reductase/1.000
3o0oTTPVitamin B12-dependent ribonucleotide reductase/0.548
3o0qTTPVitamin B12-dependent ribonucleotide reductase/0.544
5im3DTPRibonucleoside-diphosphate reductase/0.521
1xjjDGTVitamin B12-dependent ribonucleotide reductase/0.490
3oafOAGDihydrofolate reductase1.5.1.30.487
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.483
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.480
3ad9NADSubunit alpha of sarocosine oxidase/0.479
4q71FADBifunctional protein PutA/0.477
1xjkDGTVitamin B12-dependent ribonucleotide reductase/0.476
2wghDTPRibonucleoside-diphosphate reductase large subunit1.17.4.10.473
4x5gFOLDihydrofolate reductase1.5.1.30.471
3p67FMNPentaerythritol tetranitrate reductase/0.466
4bfvZVVPantothenate kinase2.7.1.330.463
3gyaCOAGCN5-related N-acetyltransferase/0.462
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.462
1e1qADPATP synthase subunit beta, mitochondrial3.6.3.140.461
1svlADPLarge T antigen3.6.40.461
5bpfADPD-alanine--D-alanine ligase/0.461
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.459
4du82P0Mevalonate diphosphate decarboxylase/0.459
1g4tFTPThiamine-phosphate synthase/0.458
3oxfSAHHistone-lysine N-methyltransferase SMYD32.1.1.430.457
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.456
4tlbAGSCircadian clock protein kinase KaiC2.7.11.10.456
1xjnDTPVitamin B12-dependent ribonucleotide reductase/0.455
2bunFADAppA protein/0.455
4g95OAGDihydrofolate reductase1.5.1.30.455
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.455
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.454
4opgFDAConserved Archaeal protein/0.454
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.452
2pdaTPPPyruvate synthase/0.452
2xh9J01Uncharacterized protein/0.451
3uhmRFNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.451
5drdATPAurora kinase A2.7.11.10.451
3av7KYAUncharacterized protein/0.449
3p62FMNPentaerythritol tetranitrate reductase/0.449
3vthAPCCarbamoyltransferase/0.449
1kzjCB3Thymidylate synthase/0.448
1s4dSAHUroporphyrinogen-III C-methyltransferase2.1.1.1070.448
1tj0FADBifunctional protein PutA1.5.5.20.448
3fhxPXLPyridoxal kinase2.7.1.350.448
3qt62P0Mevalonate diphosphate decarboxylase/0.448
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.448
4tl7ATPCircadian clock protein kinase KaiC2.7.11.10.448
4xx9ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.448
5dstSAHProtein arginine N-methyltransferase 82.1.10.448
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.447
2fy4COACholine O-acetyltransferase2.3.1.60.446
2qdxFADFerredoxin--NADP+ reductase/0.446
3da1FADGlycerol-3-phosphate dehydrogenase/0.446
2dwbANPAurora kinase A2.7.11.10.445
2w9hTOPDihydrofolate reductase1.5.1.30.445
4q72FADBifunctional protein PutA/0.445
4q73FADBifunctional protein PutA/0.445
1xddAAYIntegrin alpha-L/0.444
4dpuAGSMevalonate diphosphate decarboxylase/0.444
4kqwNAPKetol-acid reductoisomerase (NADP(+))/0.444
1a8pFADFerredoxin--NADP reductase/0.443
2cig1DGDihydrofolate reductase1.5.1.30.443
2cntCOARibosomal-protein-alanine acetyltransferase/0.443
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3p74FMNPentaerythritol tetranitrate reductase/0.443
4dxhNAJAlcohol dehydrogenase E chain1.1.1.10.443
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.443
1dr2TAPDihydrofolate reductase1.5.1.30.442
1ewyFADFerredoxin--NADP reductase1.18.1.20.442
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.442
4elb34SDihydrofolate reductase/0.442
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.441
1h50FMNPentaerythritol tetranitrate reductase/0.441
2tpsTPSThiamine-phosphate synthase/0.441
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.441
3a20FMNFMN-binding protein/0.441
3ddpRC8Cyclin-dependent kinase 22.7.11.220.441
4bwxAGSPAB-dependent poly(A)-specific ribonuclease subunit pan3/0.441
4oa9ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.441
1dr3HBIDihydrofolate reductase1.5.1.30.440
1vyrFMNPentaerythritol tetranitrate reductase/0.440
1vyw292Cyclin-dependent kinase 22.7.11.220.440
2r1rTTPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.440
4dymIYZActivin receptor type-12.7.11.300.440
4k33ACPFibroblast growth factor receptor 32.7.10.10.440