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 |
|---|---|---|---|
| 4cry | ACO | PanD regulatory factor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4cry | ACO | PanD regulatory factor | / | 1.000 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.631 | |
| 4crz | ACO | PanD regulatory factor | / | 0.601 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.537 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.530 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.527 | |
| 2wpw | ACO | Orf14 | / | 0.513 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.511 | |
| 2wpx | ACO | Orf14 | / | 0.508 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.506 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.505 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.502 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.498 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.497 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.494 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.492 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.492 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.490 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.489 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.484 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.482 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.482 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.481 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.481 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.474 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.474 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.470 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.470 | |
| 5kf2 | COA | Predicted acetyltransferase | / | 0.469 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.468 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.468 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.466 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.466 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.466 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.465 | |
| 3wow | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.464 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.462 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.461 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.461 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.460 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.460 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.460 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.459 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1jut | LYD | Thymidylate synthase | / | 0.458 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.458 | |
| 1pkd | UCN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.458 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.458 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.458 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.457 | |
| 1f28 | UMP | Thymidylate synthase | 2.1.1.45 | 0.456 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.456 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.455 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.454 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.454 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.454 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 1kgj | FL8 | Transthyretin | / | 0.453 | |
| 4eqr | FAD | Coenzyme A disulfide reductase | / | 0.453 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.453 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 3f8k | COA | Uncharacterized protein | / | 0.452 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.452 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.452 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 0.451 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.451 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 1juj | LYA | Thymidylate synthase | 2.1.1.45 | 0.450 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 2og8 | 1N8 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.450 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.450 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.450 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.449 | |
| 2wue | KEK | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.449 | |
| 3c1x | CKK | Hepatocyte growth factor receptor | 2.7.10.1 | 0.449 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.449 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.449 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.448 | |
| 1f28 | F89 | Thymidylate synthase | 2.1.1.45 | 0.448 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.448 | |
| 2wug | HPK | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.448 | |
| 3amy | AGI | Casein kinase II subunit alpha | 2.7.11.1 | 0.448 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.447 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.447 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.447 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.447 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.447 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.446 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.446 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.446 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.446 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.446 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.446 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.446 | |
| 5ckw | ANP | Uncharacterized protein | / | 0.446 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.445 | |
| 3b9l | AZZ | Serum albumin | / | 0.445 | |
| 3wsb | RWZ | Farnesyltransferase, putative | / | 0.445 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.444 | |
| 3zp4 | TSA | Chorismate mutase AroH | 5.4.99.5 | 0.444 | |
| 1syn | F89 | Thymidylate synthase | / | 0.443 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2bxq | IMN | Serum albumin | / | 0.443 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.443 | |
| 3c3e | GDP | 2-phospho-L-lactate transferase | / | 0.443 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3up0 | D7S | aceDAF-12 | / | 0.443 | |
| 3upy | FOM | Oxidoreductase, putative | / | 0.443 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.443 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.443 | |
| 4b99 | R4L | Mitogen-activated protein kinase 7 | 2.7.11.24 | 0.443 | |
| 4bch | T7Z | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.443 | |
| 4pd6 | URI | Nucleoside permease | / | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.442 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.442 | |
| 4bcq | TJF | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4ogr | ADN | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.442 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.441 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.441 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.441 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.441 | |
| 4gt3 | ATP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.441 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.440 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.440 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.440 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 4j26 | EST | Estrogen receptor beta | / | 0.440 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.440 |