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 |
|---|---|---|---|
| 5dsg | 0HK | Muscarinic acetylcholine receptor M4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5dsg | 0HK | Muscarinic acetylcholine receptor M4 | / | 1.000 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.623 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.593 | |
| 4daj | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.573 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.526 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.496 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.494 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.487 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.483 | |
| 3bmq | AX5 | Pteridine reductase | / | 0.483 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.480 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.475 | |
| 3nwl | NDP | Catalase | 1.11.1.6 | 0.473 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.471 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.471 | |
| 4u15 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.470 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.469 | |
| 1t40 | ID5 | Aldose reductase | 1.1.1.21 | 0.468 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.467 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.466 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.466 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 1u08 | PLP | Methionine aminotransferase | / | 0.465 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.465 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.464 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.463 | |
| 4j7h | TRH | PCZA361.3 | / | 0.463 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.462 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.462 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.462 | |
| 4hcy | 0YN | Transketolase | / | 0.462 | |
| 1qv0 | CZH | Obelin | / | 0.461 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.460 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.460 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.458 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.458 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.457 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.457 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.456 | |
| 2qjp | ANJ | Cytochrome b | / | 0.456 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.456 | |
| 2dv0 | ZST | Aldose reductase | 1.1.1.21 | 0.455 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 4isf | 1FX | Glucokinase | 2.7.1.2 | 0.455 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.455 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.454 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.454 | |
| 4u95 | MIY | Multidrug efflux pump subunit AcrB | / | 0.454 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.453 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.453 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.453 | |
| 3c1o | NAP | Eugenol synthase | / | 0.453 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.453 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.453 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.453 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.453 | |
| 5d7p | AR6 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.453 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.452 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.452 | |
| 4jvm | XDI | Estrogen sulfotransferase | 2.8.2.4 | 0.452 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.451 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.451 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.451 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.451 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.451 | |
| 1jf2 | CZH | Obelin | / | 0.450 | |
| 1qv1 | CZH | Obelin | / | 0.450 | |
| 1s36 | CEI | Obelin | / | 0.450 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.450 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.450 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.449 | |
| 1z3n | 3NA | Aldose reductase | 1.1.1.21 | 0.449 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.449 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.449 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.449 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.448 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.448 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.448 | |
| 1g3m | PCQ | Estrogen sulfotransferase | 2.8.2.4 | 0.447 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.447 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4i5x | FLF | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.447 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.447 | |
| 4oe4 | NAD | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial | 1.2.1.88 | 0.447 | |
| 2z4w | 749 | Geranylgeranyl pyrophosphate synthase | / | 0.446 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.446 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.446 | |
| 5liu | 388 | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.446 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.445 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.445 | |
| 1giq | NAI | Iota toxin component Ia | / | 0.444 | |
| 1lke | DOG | Bilin-binding protein | / | 0.444 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.444 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.443 | |
| 2ewa | SB2 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.443 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.443 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.443 | |
| 4jtr | IBP | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.442 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1s07 | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.442 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.442 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2ipj | FFA | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 4je5 | PLP | Aromatic/aminoadipate aminotransferase 1 | 2.6.1.39 | 0.442 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.441 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.441 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.441 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.441 | |
| 4h6p | FMN | Chromate reductase | / | 0.441 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.441 | |
| 4odo | FK5 | Peptidyl-prolyl cis-trans isomerase | / | 0.441 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.440 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.440 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.440 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.440 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.440 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.440 |