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 |
|---|---|---|---|
| 4da5 | 0H7 | Choline kinase alpha | 2.7.1.32 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4da5 | 0H7 | Choline kinase alpha | 2.7.1.32 | 1.000 | |
| 4br3 | U85 | Choline kinase alpha | 2.7.1.32 | 0.590 | |
| 3zm9 | QMQ | Choline kinase alpha | 2.7.1.32 | 0.538 | |
| 4cg8 | G8S | Choline kinase alpha | 2.7.1.32 | 0.515 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.509 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.499 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.497 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.494 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.490 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.489 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.489 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.488 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.486 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.486 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.485 | |
| 4xt8 | TMQ | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.484 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.483 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.482 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.482 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.481 | |
| 3mes | PT3 | Putative choline kinase | / | 0.481 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.479 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 2ipj | FFA | Aldo-keto reductase family 1 member C2 | / | 0.476 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.476 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.471 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.470 | |
| 3i0o | SMI | Spectinomycin phosphotransferase | / | 0.468 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.467 | |
| 1x2e | ATX | Proline iminopeptidase | 3.4.11.5 | 0.466 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.466 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.465 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.464 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.464 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.464 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.463 | |
| 1s0j | MUS | Trans-sialidase | / | 0.463 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 1xid | ASC | Xylose isomerase | 5.3.1.5 | 0.461 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 3fi8 | OPE | Choline kinase | / | 0.460 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.460 | |
| 4f1q | 0RZ | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.460 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.460 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.459 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.459 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.459 | |
| 3w2e | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.459 | |
| 4qfx | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.459 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.458 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.458 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1x2b | STX | Proline iminopeptidase | 3.4.11.5 | 0.457 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.457 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.457 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.457 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.457 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.456 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3g5e | Q74 | Aldose reductase | 1.1.1.21 | 0.456 | |
| 3gf4 | U5P | UDP-galactopyranose mutase | 5.4.99.9 | 0.456 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.456 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2wea | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.455 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.455 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.455 | |
| 4nhy | PD2 | Prolyl 3-hydroxylase OGFOD1 | 1.14.11 | 0.455 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 4j7h | TRH | PCZA361.3 | / | 0.454 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.453 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.453 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.453 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.453 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4daj | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.453 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.452 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.452 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.452 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.452 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.452 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 4a7y | NHF | Aldos-2-ulose dehydratase | / | 0.452 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.451 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.451 | |
| 1e6z | NGO | Chitinase | / | 0.450 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.450 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.450 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.450 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 3hr4 | FMN | Nitric oxide synthase, inducible | 1.14.13.39 | 0.450 | |
| 4adc | PLP | Succinylornithine transaminase | 2.6.1.81 | 0.450 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.450 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.449 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.449 | |
| 3myt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.449 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.449 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.449 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 2v8p | CDP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 4je5 | PLP | Aromatic/aminoadipate aminotransferase 1 | 2.6.1.39 | 0.448 | |
| 4jtq | FLP | Aldo-keto reductase family 1 member C2 | / | 0.448 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.448 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.448 | |
| 1a26 | CNA | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.447 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4jtr | IZP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3g5i | DNB | Pyrimidine-specific ribonucleoside hydrolase RihA | / | 0.446 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.446 | |
| 3ugr | IMN | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.446 | |
| 4ts7 | ADP | Purine phosphoribosyltransferase (GpT-1) | / | 0.446 | |
| 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 | 0.445 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.444 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.444 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.444 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4a7z | AY9 | Aldos-2-ulose dehydratase | / | 0.443 | |
| 4iil | RBF | Membrane lipoprotein TpN38(b) | / | 0.443 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.442 | |
| 1kqg | HQO | Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit | / | 0.442 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 2d2g | DZZ | Phosphotriesterase | / | 0.442 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.442 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3c72 | CX1 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.441 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.441 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.441 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4lrh | FOL | Folate receptor alpha | / | 0.441 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.440 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.440 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.440 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3b4p | 3B4 | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.440 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3p5l | IT5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.440 | |
| 4xcz | T3Q | Qdtf | / | 0.440 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.440 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.440 |