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 |
|---|---|---|---|
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 1.000 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.514 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.503 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.492 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.492 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.488 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.485 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.485 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.479 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.477 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.477 | |
| 1fml | RTL | Retinol dehydratase | / | 0.476 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.472 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.472 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.471 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.470 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.469 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.468 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.468 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.467 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.467 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.466 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.466 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.466 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.465 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.465 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.464 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.463 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.462 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.462 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.461 | |
| 1a26 | CNA | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.459 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.459 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.459 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.459 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.459 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.459 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.459 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.458 | |
| 3arv | SAU | Chitinase A | / | 0.458 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.458 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.457 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.457 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.457 | |
| 1b9i | PXG | 3-amino-5-hydroxybenzoate synthase | 4.2.1.144 | 0.456 | |
| 2iej | S48 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.456 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.455 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.455 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.455 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.455 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.455 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.454 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.454 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.454 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 3c1o | NAP | Eugenol synthase | / | 0.453 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.453 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.453 | |
| 4bub | ADP | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase | / | 0.453 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.452 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.452 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.452 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.452 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.452 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.452 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.452 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.451 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 3arp | DEQ | Chitinase A | / | 0.451 | |
| 3wag | TYD | Glycosyltransferase | / | 0.451 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.450 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.450 | |
| 1ycf | FMN | Nitric oxide reductase | 1 | 0.450 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.450 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.449 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.449 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.449 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.449 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.449 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.448 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.448 | |
| 3pbl | ETQ | D(3) dopamine receptor | / | 0.448 | |
| 2pk3 | GDD | GDP-6-deoxy-D-mannose reductase | / | 0.447 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.447 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 2fzd | TOL | Aldose reductase | 1.1.1.21 | 0.446 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.446 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.446 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.445 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.445 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.445 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.445 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.445 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.445 | |
| 4zas | TYD | CalS13 | / | 0.445 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.444 | |
| 1v08 | NTZ | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.444 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.444 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.444 | |
| 4usr | FAD | Monooxygenase | / | 0.444 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.443 | |
| 1lc3 | NAD | Biliverdin reductase A | 1.3.1.24 | 0.443 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.443 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.443 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.443 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.443 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.443 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.442 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2ejz | SAH | Diphthine synthase | / | 0.442 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.442 | |
| 2vuu | NAP | Nitrogen metabolite repression protein nmrA | / | 0.442 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.442 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4hhy | 15R | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.442 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.441 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2vt4 | P32 | Beta-1 adrenergic receptor | / | 0.441 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3b05 | IPE | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 3ndj | JHZ | Methyltransferase | / | 0.441 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.441 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.440 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.440 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.440 | |
| 4je5 | PLP | Aromatic/aminoadipate aminotransferase 1 | 2.6.1.39 | 0.440 |