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 |
|---|---|---|---|
| 3fsu | C2F | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3fsu | C2F | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 1.000 | |
| 1zp4 | C2F | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.513 | |
| 2fmn | 4HF | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.504 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.484 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.481 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.481 | |
| 3qly | 55V | Uncharacterized protein | / | 0.476 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.475 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.474 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.470 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.468 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.468 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.467 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.466 | |
| 3fc1 | 52P | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.464 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.463 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.463 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.462 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.462 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.462 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.461 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.459 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.459 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.459 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 1uze | EAL | Angiotensin-converting enzyme | 3.2.1 | 0.458 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.458 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.458 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.457 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.457 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.457 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.456 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.456 | |
| 4h4u | NDP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.456 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 1tl1 | H18 | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.454 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.453 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.453 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.453 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.453 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.453 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 2bx8 | AZQ | Serum albumin | / | 0.452 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.452 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.452 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 4grb | 0XG | Casein kinase II subunit alpha | 2.7.11.1 | 0.452 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.452 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.451 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.451 | |
| 1osv | CHC | Bile acid receptor | / | 0.451 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.451 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.451 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.451 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.451 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.451 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.450 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.450 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.450 | |
| 4bqp | VMY | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 4g1w | G1W | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.450 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.449 | |
| 2cmw | OLP | Casein kinase I isoform gamma-1 | 2.7.11.1 | 0.449 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.449 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3jw5 | TOP | Dihydrofolate reductase | / | 0.449 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.448 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.448 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.448 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.448 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.448 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 1heu | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1s6q | TPB | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.447 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.447 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.447 | |
| 3roc | 29A | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.447 | |
| 4e73 | 0NR | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.447 | |
| 1fml | RTL | Retinol dehydratase | / | 0.446 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1ppj | ANY | Cytochrome b | / | 0.446 | |
| 1tdu | DUR | Thymidylate synthase | / | 0.446 | |
| 1yw2 | PGJ | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.446 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.446 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 4ii5 | ADP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.445 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 2bj4 | OHT | Estrogen receptor | / | 0.445 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.445 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.445 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.445 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.445 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.445 | |
| 5kjc | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.444 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2itt | AEE | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.444 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.444 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.444 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.444 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.443 | |
| 1tl3 | H20 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.443 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.443 | |
| 3cse | N22 | Uncharacterized protein | / | 0.443 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.443 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.443 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.443 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.443 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.442 | |
| 1eio | GCH | Gastrotropin | / | 0.442 | |
| 1iky | MSD | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 1ju6 | LYA | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2acw | UPG | Glycosyltransferase | / | 0.442 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2bun | FAD | AppA protein | / | 0.442 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.442 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.442 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.442 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.442 | |
| 3a4p | DFQ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 3h1j | SMA | Cytochrome b | / | 0.442 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.442 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.442 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.442 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 4h50 | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.442 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.441 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.441 | |
| 2wug | HPK | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.441 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3i0r | RT3 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.441 | |
| 3n0t | OPY | Dipeptidyl peptidase 2 | 3.4.14.2 | 0.441 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.441 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.441 | |
| 3zw9 | T1G | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.441 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.441 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.441 | |
| 1ezv | SMA | Cytochrome b | / | 0.440 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.440 | |
| 1pp9 | SMA | Cytochrome b | / | 0.440 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.440 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.440 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.440 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.440 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3ely | SAH | Methyltransferase | / | 0.440 | |
| 3iqf | E4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.440 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.440 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.440 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.440 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.440 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3zux | TCH | Transporter | / | 0.440 | |
| 4a1z | ADP | Kinesin-like protein KIF11 | / | 0.440 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.440 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 4pd6 | URI | Nucleoside permease | / | 0.440 |