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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
1d0vRBZNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.21

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1d0vRBZNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.211.000
1jhaAAMNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.734
1l4gNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.680
1l5k1RBNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.672
1l4kNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.667
1l4hNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.664
1jhrP2PNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.660
1l4mNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.633
1l4fNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.602
1l4lNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.574
1l5m7RANicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.549
1l4eRBZNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.524
1jhqPMONicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.522
1l5oNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.484
1xe55FEPlasmepsin-23.4.23.390.479
1oc1ASVIsopenicillin N synthase1.21.3.10.475
2eq6FADDihydrolipoyl dehydrogenase/0.474
4du82P0Mevalonate diphosphate decarboxylase/0.466
4ips1G4Mycocyclosin synthase1.14.21.90.464
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.463
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.461
1obnASVIsopenicillin N synthase1.21.3.10.460
2fy4COACholine O-acetyltransferase2.3.1.60.459
4ktf1TMCytochrome P450/0.459
2xfsJ01Uncharacterized protein/0.458
3zoiM2WIsopenicillin N synthase1.21.3.10.458
4a8v2ANMajor pollen allergen Bet v 1-J/0.458
3gqvNAPEnoyl reductase LovC10.457
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.457
2e0nSAHPrecorrin-2 C20-methyltransferase/0.456
2vcmM11Isopenicillin N synthase1.21.3.10.456
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.456
3nl6TPSUncharacterized protein/0.456
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.456
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.455
2yj4ATPCopper-transporting ATPase/0.455
3gviADPMalate dehydrogenase/0.455
2wo7ASVIsopenicillin N synthase1.21.3.10.454
3t3q9PLCytochrome P450 2A61.14.130.454
4ktl1CQCytochrome P450/0.454
1meiXMPInosine-5'-monophosphate dehydrogenase/0.453
1owmFADDeoxyribodipyrimidine photo-lyase4.1.99.30.453
1tehNADAlcohol dehydrogenase class-31.1.1.10.453
4g48PZBMycocyclosin synthase1.14.21.90.453
3ixp834Ecdysone receptor/0.452
3adaNADSubunit alpha of sarocosine oxidase/0.451
3g5hYTTMycocyclosin synthase1.14.21.90.451
1t85CAMCamphor 5-monooxygenase1.14.15.10.450
2ccu2D9Heat shock protein HSP 90-alpha/0.450
3oibFDAPutative acyl-CoA dehydrogenase/0.450
4uyf73BBromodomain-containing protein 2/0.450
1dz4CAMCamphor 5-monooxygenase1.14.15.10.449
2y6fM9FIsopenicillin N synthase1.21.3.10.449
4rcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.449
4ea30NNNociceptin receptor/0.449
2xh9J01Uncharacterized protein/0.448
3s1dZIRCytokinin dehydrogenase 11.5.99.120.448
4i02CMPcAMP-activated global transcriptional regulator CRP/0.448
1fmjRTLRetinol dehydratase/0.447
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.447
3hl0NADMaleylacetate reductase/0.447
4y8wSTRSteroid 21-hydroxylase/0.447
1blzACVIsopenicillin N synthase1.21.3.10.446
3tjzGNPADP-ribosylation factor 1/0.446
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.445
1lsoNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1mokFAD2-oxopropyl-CoM reductase, carboxylating1.8.1.50.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.444
2nq8ZIDEnoyl-ACP reductase/0.444
3t3r9PLCytochrome P450 2A61.14.130.444
3zh8C58Protein kinase C iota type2.7.11.130.444
4ipw1G7Mycocyclosin synthase1.14.21.90.444
4nbwNADShort-chain dehydrogenase/reductase SDR/0.444
5k5zANPUncharacterized protein/0.444
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.443
2givACOHistone acetyltransferase KAT8/0.443
2q4bNAPUncharacterized protein At5g02240/0.443
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.443
2zgyGDPPlasmid segregation protein ParM/0.443
3kduNKSPeroxisome proliferator-activated receptor alpha/0.443
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4fmxCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.443
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
1dg8NDPDihydrofolate reductase1.5.1.30.442
1dhrNADDihydropteridine reductase1.5.1.340.442
1v35NAIEnoyl-ACP reductase/0.442
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
2y4gTIRTamL/0.442
3b70NAPEnoyl reductase LovC10.442
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.442
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.442
4q72FADBifunctional protein PutA/0.442
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
2gjnFMNNitronate monooxygenase1.13.12.160.441
3i6iNDPPutative leucoanthocyanidin reductase 1/0.441
3oafOAGDihydrofolate reductase1.5.1.30.441
4jdrFADDihydrolipoyl dehydrogenase1.8.1.40.441
4lb2DM5Serum albumin/0.441
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
1t13INI6,7-dimethyl-8-ribityllumazine synthase 2/0.440
1xq6NAPUncharacterized protein At5g02240/0.440
3a9wNADNDP-sugar epimerase/0.440
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.440
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.440
4jldADPAdenylate kinase/0.440