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 |
|---|---|---|---|
| 1c23 | MPH | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1c23 | MPH | Methionine aminopeptidase | / | 1.000 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.646 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.637 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.627 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.624 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.619 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.614 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.612 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.612 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.611 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.609 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.604 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.603 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.602 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.602 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.596 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.592 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.591 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.590 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.590 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.590 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.589 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.588 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.584 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.580 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.578 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.559 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.558 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.556 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.553 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.547 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.532 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.530 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.520 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.509 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.499 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.498 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.497 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.488 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.483 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.482 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.472 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.472 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.471 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.470 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.470 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.469 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.469 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.469 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.468 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.467 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.466 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1e6z | NGO | Chitinase | / | 0.463 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.463 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.462 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.462 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.462 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.461 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.461 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.461 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.460 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.459 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.459 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.459 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.458 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.458 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.457 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.456 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3v2u | ATP | Protein GAL3 | / | 0.456 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1ndi | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.454 | |
| 3tdv | GDP | Gentamicin resistance protein | / | 0.454 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.454 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.453 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.452 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.452 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.452 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.450 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.450 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.449 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.449 | |
| 3r8h | ZOM | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.449 | |
| 3vet | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.449 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.449 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.448 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2wvm | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.448 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3e6e | DCS | Alanine racemase | / | 0.448 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.447 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.447 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.447 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.447 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.446 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.446 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.445 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.445 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.444 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2z4w | 749 | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.443 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.443 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.443 | |
| 2iu8 | UD1 | UDP-3-O-acylglucosamine N-acyltransferase | 2.3.1 | 0.443 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.443 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1j37 | X8Z | Angiotensin-converting enzyme | 3.4.15.1 | 0.442 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.442 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.442 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.442 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.441 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.441 | |
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.441 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |