sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4gkm | 683 | Anthranilate phosphoribosyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4gkm | 683 | Anthranilate phosphoribosyltransferase | / | 1.000 | |
| 3r6c | 17N | Anthranilate phosphoribosyltransferase | / | 0.561 | |
| 3qqs | 17C | Anthranilate phosphoribosyltransferase | / | 0.560 | |
| 3qsa | TA7 | Anthranilate phosphoribosyltransferase | / | 0.533 | |
| 4giu | 636 | Anthranilate phosphoribosyltransferase | / | 0.528 | |
| 3qs8 | 17D | Anthranilate phosphoribosyltransferase | / | 0.527 | |
| 4ztv | TA7 | Anthranilate phosphoribosyltransferase | / | 0.513 | |
| 3uu1 | 14B | Anthranilate phosphoribosyltransferase | / | 0.508 | |
| 4ij1 | 17C | Anthranilate phosphoribosyltransferase | / | 0.508 | |
| 3r88 | 14F | Anthranilate phosphoribosyltransferase | / | 0.503 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.491 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.483 | |
| 4own | 5RG | Anthranilate phosphoribosyltransferase | / | 0.478 | |
| 3eku | CY9 | Actin-5C | / | 0.472 | |
| 4ubt | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.469 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.467 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2r8v | ACO | Amino-acid acetyltransferase | / | 0.466 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 4coj | DTP | Uncharacterized protein | / | 0.465 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.463 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.463 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.462 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.462 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.461 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.461 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.459 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.458 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.457 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.457 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 4y6u | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.457 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.456 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.456 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4biw | ANP | Sensor histidine kinase CpxA | / | 0.455 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.455 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.455 | |
| 4to3 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.455 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.454 | |
| 3qtt | ANP | Pantothenate synthetase | / | 0.454 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.454 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.453 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.452 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.452 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.452 | |
| 2vcx | D26 | Hematopoietic prostaglandin D synthase | / | 0.452 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.452 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.452 | |
| 4pkw | GM6 | Lethal factor | 3.4.24.83 | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.451 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.451 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.451 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.450 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.450 | |
| 2qs1 | UB1 | Glutamate receptor ionotropic, kainate 1 | / | 0.449 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.449 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.449 | |
| 4h4u | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.449 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.449 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.449 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.448 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.448 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.448 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.448 | |
| 3eks | CY9 | Actin-5C | / | 0.448 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.448 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.448 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.448 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.447 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.447 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta | / | 0.447 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta' | / | 0.447 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.447 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.446 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.446 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.446 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.445 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3gob | HXX | DdmC | / | 0.445 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.445 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.445 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.445 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.444 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.444 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.444 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.444 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.443 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.443 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.443 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.443 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.443 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.443 | |
| 3zxs | FAD | Deoxyribodipyrimidine photolyase-related protein | / | 0.443 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4hn1 | TYD | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.443 | |
| 4qxq | 1YE | Stimulator of interferon genes protein | / | 0.443 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.443 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2bxf | DZP | Serum albumin | / | 0.442 | |
| 2y3r | TIR | TamL | / | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.442 | |
| 4gn6 | TYL | Lactoperoxidase | 1.11.1.7 | 0.442 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.442 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.442 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.441 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.441 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.441 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.441 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.441 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.440 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.440 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.440 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.440 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 4qfx | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 | |
| 4y8v | ADP | Acyl-CoA synthetase (NDP forming) | / | 0.440 |