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 |
|---|---|---|---|
| 4zhi | ADP | Kinesin-like protein KIF11 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4zhi | ADP | Kinesin-like protein KIF11 | / | 1.000 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.492 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.486 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.484 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.481 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.481 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.478 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.476 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.476 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.474 | |
| 1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.473 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.473 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.473 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.472 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.471 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.471 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.471 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2obx | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | 2.5.1.78 | 0.468 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.466 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.466 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.463 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.462 | |
| 1t13 | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | / | 0.462 | |
| 2b03 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.462 | |
| 2pg2 | ADP | Kinesin-like protein KIF11 | / | 0.462 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.462 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.461 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 4f0f | ACP | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.458 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.458 | |
| 4qjq | OTR | Lactoperoxidase | / | 0.458 | |
| 3k9v | CPS | 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial | / | 0.457 | |
| 3l9h | ADP | Kinesin-like protein KIF11 | / | 0.457 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.457 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.456 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.455 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.454 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.453 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 1uhl | MEI | Retinoic acid receptor RXR-beta | / | 0.451 | |
| 3cgy | RDC | Virulence sensor histidine kinase PhoQ | 2.7.13.3 | 0.451 | |
| 4fw0 | 5KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.451 | |
| 4p6w | MOF | Glucocorticoid receptor | / | 0.451 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.451 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.450 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.450 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.450 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.450 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1rx6 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.449 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.449 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.449 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.449 | |
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 0.448 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.448 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.448 | |
| 2owb | 626 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.448 | |
| 2xae | ADP | Kinesin-like protein KIF11 | / | 0.448 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.448 | |
| 3p9t | TCL | Repressor | / | 0.448 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.448 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.448 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2xkd | T3M | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.447 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 3fal | REA | Retinoic acid receptor RXR-alpha | / | 0.447 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.447 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.447 | |
| 5bn4 | ANP | V-type ATP synthase alpha chain | / | 0.447 | |
| 1fml | RTL | Retinol dehydratase | / | 0.446 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2acl | REA | Retinoic acid receptor RXR-alpha | / | 0.446 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 2jed | LG8 | Protein kinase C theta type | 2.7.11.13 | 0.446 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.446 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.446 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.446 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.445 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3zkp | ERB | Erythromycin C-12 hydroxylase | 1.14.13.154 | 0.445 | |
| 4a4l | 939 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.445 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.444 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.444 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.444 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.444 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.444 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.444 | |
| 1q3w | ATU | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.443 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.442 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.441 | |
| 1m9m | 6NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.441 | |
| 1owp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.441 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.441 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4dvq | 1CA | Cytochrome P450 11B2, mitochondrial | 1.14.15.4 | 0.441 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2olc | ADP | Methylthioribose kinase | 2.7.1.100 | 0.440 | |
| 3dxm | N24 | Actin-related protein 3 | / | 0.440 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.440 | |
| 4g1n | NZT | Pyruvate kinase PKM | 2.7.1.40 | 0.440 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.440 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.440 |