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 |
|---|---|---|---|
| 2q2y | ADP | Kinesin-like protein KIF11 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2q2y | ADP | Kinesin-like protein KIF11 | / | 1.000 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.608 | |
| 2fl2 | ADP | Kinesin-like protein KIF11 | / | 0.603 | |
| 2pg2 | ADP | Kinesin-like protein KIF11 | / | 0.592 | |
| 2xae | ADP | Kinesin-like protein KIF11 | / | 0.572 | |
| 3l9h | ADP | Kinesin-like protein KIF11 | / | 0.550 | |
| 2q2z | ADP | Kinesin-like protein KIF11 | / | 0.542 | |
| 2x7e | ADP | Kinesin-like protein KIF11 | / | 0.535 | |
| 4zhi | ADP | Kinesin-like protein KIF11 | / | 0.528 | |
| 2x2r | ADP | Kinesin-like protein KIF11 | / | 0.522 | |
| 3hqd | ANP | Kinesin-like protein KIF11 | / | 0.512 | |
| 4ap0 | ADP | Kinesin-like protein KIF11 | / | 0.501 | |
| 2g1q | ADP | Kinesin-like protein KIF11 | / | 0.495 | |
| 4a51 | ADP | Kinesin-like protein KIF11 | / | 0.494 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.492 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.492 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.489 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.481 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.477 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.475 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.474 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.473 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.472 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 2xk3 | XK3 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.471 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.470 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.470 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.468 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.468 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.467 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.466 | |
| 1syn | F89 | Thymidylate synthase | / | 0.465 | |
| 1mj3 | HXC | Enoyl-CoA hydratase, mitochondrial | 4.2.1.17 | 0.464 | |
| 3htj | ET | EbrA repressor | / | 0.464 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.463 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.463 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1w2c | ANP | Inositol-trisphosphate 3-kinase A | 2.7.1.127 | 0.462 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.461 | |
| 4gqk | ADP | Actin cross-linking toxin VgrG1 | / | 0.461 | |
| 1jxz | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.460 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.460 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.460 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.460 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 4b7b | ADP | Kinesin-like protein KIF11 | / | 0.460 | |
| 4hqv | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.459 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.458 | |
| 2xk8 | 5R1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.457 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.457 | |
| 4q15 | HFG | Proline--tRNA ligase | 6.1.1.15 | 0.457 | |
| 2h2e | SA8 | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.456 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.456 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4bwa | N0B | Pyrrolysine--tRNA ligase | / | 0.456 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.456 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.455 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.455 | |
| 1uhl | MEI | Retinoic acid receptor RXR-beta | / | 0.454 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2zfi | ADP | Kinesin-like protein KIF1A | / | 0.454 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.454 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.454 | |
| 4g1n | NZT | Pyruvate kinase PKM | 2.7.1.40 | 0.454 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.453 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.452 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.452 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.452 | |
| 2mm3 | CHO | Gastrotropin | / | 0.452 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.452 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.452 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4qij | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.452 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.451 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4afe | GGY | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.451 | |
| 4uof | DAT | Nucleoside diphosphate kinase | / | 0.451 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2b04 | CHO | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.450 | |
| 4f1t | H52 | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.450 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 4m6k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.449 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4f1m | ACP | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.449 | |
| 2x9v | TMQ | Pteridine reductase | / | 0.448 | |
| 2xk7 | 30E | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.448 | |
| 3p9t | TCL | Repressor | / | 0.448 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.448 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 3ele | PLP | Aminotransferase | / | 0.447 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.447 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4qii | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.447 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.447 | |
| 1nzy | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.446 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 2wky | IBC | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 4b6l | 9ZP | Serine/threonine-protein kinase PLK3 | 2.7.11.21 | 0.446 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.446 | |
| 4kfj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4m8h | R4M | Retinoic acid receptor RXR-alpha | / | 0.446 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.445 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.445 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.444 | |
| 1wpg | ADP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.444 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1zy5 | ANP | eIF-2-alpha kinase GCN2 | / | 0.444 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.444 | |
| 3fra | I2H | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.444 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2bif | ANP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.443 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.443 | |
| 3be2 | RAJ | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.443 | |
| 3gie | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.443 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.443 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.442 | |
| 1u72 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2ewa | SB2 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.442 | |
| 1ne6 | SP1 | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.441 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1f3e | DPZ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.440 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.440 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2o28 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.440 | |
| 2pda | TPP | Pyruvate synthase | / | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.440 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.440 |