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 |
|---|---|---|---|
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 1.000 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.725 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.721 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.647 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.629 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.589 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.582 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.572 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.561 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.556 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.543 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.524 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.521 | |
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.513 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.512 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.505 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.502 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.497 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.488 | |
| 1b8o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.485 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.485 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.482 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.478 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.477 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.477 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.475 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.474 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.470 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.467 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3v2u | ATP | Protein GAL3 | / | 0.465 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.462 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.461 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.459 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1a9s | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.458 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.458 | |
| 3f8w | ADN | Purine nucleoside phosphorylase | / | 0.458 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.458 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.458 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.457 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.456 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.455 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.455 | |
| 2ejz | SAH | Diphthine synthase | / | 0.454 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.452 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.451 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.449 | |
| 2dvo | ITT | dITP/XTP pyrophosphatase | 3.6.1.19 | 0.449 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.448 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.448 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4j7h | TRH | PCZA361.3 | / | 0.448 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.447 | |
| 3u8l | 09Q | Acetylcholine-binding protein | / | 0.447 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.446 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.445 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4h6p | FMN | Chromate reductase | / | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.444 | |
| 4e2b | FMN | Dehydrogenase | / | 0.444 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.443 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.442 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.441 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.440 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.440 |