sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2v95 | HCY | Corticosteroid-binding globulin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2v95 | HCY | Corticosteroid-binding globulin | / | 1.000 | |
| 2vdy | HCY | Corticosteroid-binding globulin | / | 0.511 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.499 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.496 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.496 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.481 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.478 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.476 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.474 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.474 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.472 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.471 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.471 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.471 | |
| 1rfq | LAR | Actin, alpha skeletal muscle | / | 0.469 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.469 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.468 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.467 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.467 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.466 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.466 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.465 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.464 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.463 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.462 | |
| 4eil | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.460 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.458 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.457 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.456 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.456 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.456 | |
| 4a5l | NDP | Thioredoxin reductase | / | 0.456 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.455 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.455 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.453 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.452 | |
| 2plm | SIB | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | 3.5.4.28 | 0.452 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.452 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.452 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.451 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3b9l | AZZ | Serum albumin | / | 0.451 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.451 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.450 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.450 | |
| 3lit | E15 | Protease | / | 0.450 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.449 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4v01 | 0LI | Fibroblast growth factor receptor 1 (Fms-related tyrosine kinase 2, Pfeiffer syndrome), isoform CRA_b | / | 0.449 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.449 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.448 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.448 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.448 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.448 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 2fto | TMP | Thymidylate synthase | / | 0.447 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.447 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.446 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.446 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 2bxm | IMN | Serum albumin | / | 0.446 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.445 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.445 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.444 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.444 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.444 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.443 | |
| 1k9s | FM2 | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.443 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.443 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 5flt | VJJ | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1if5 | FBT | Carbonic anhydrase 2 | 4.2.1.1 | 0.442 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.441 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4isu | IKM | Glutamate receptor 2 | / | 0.441 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.441 | |
| 4u7w | NDP | MxaA | / | 0.441 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.440 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.440 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.440 | |
| 4zas | TYD | CalS13 | / | 0.440 |