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 |
|---|---|---|---|
| 4cvb | PQQ | Alcohol dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4cvb | PQQ | Alcohol dehydrogenase | / | 1.000 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.486 | |
| 2kce | D16 | Thymidylate synthase | / | 0.474 | |
| 1aiq | CB3 | Thymidylate synthase | / | 0.469 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.468 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 4h6p | FMN | Chromate reductase | / | 0.465 | |
| 3er9 | 3AT | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.464 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.463 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.462 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.461 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.461 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.460 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.459 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.458 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.458 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2vf0 | F89 | Thymidylate synthase | / | 0.457 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4f70 | 0ST | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.456 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.455 | |
| 1tlc | F89 | Thymidylate synthase | / | 0.455 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.455 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.454 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.454 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.452 | |
| 3rim | TPP | Transketolase | 2.2.1.1 | 0.451 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.450 | |
| 3dpd | 41A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4o7u | THF | Thymidylate synthase | / | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.449 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1vrq | FMN | Subunit alpha of sarocosine oxidase | / | 0.449 | |
| 1vrq | FMN | Subunit beta of sarcosine oxidase | / | 0.449 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.449 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.449 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.448 | |
| 1syn | F89 | Thymidylate synthase | / | 0.448 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.448 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4l4x | NDP | AmphI | / | 0.448 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 2ga9 | AGS | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.447 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 2vax | CSC | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.447 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.447 | |
| 4edz | 0O5 | Hematopoietic prostaglandin D synthase | / | 0.447 | |
| 1dd6 | MCI | Metallo-beta-lactamase type 2 | / | 0.446 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.446 | |
| 1lua | NAP | Bifunctional protein MdtA | 1.5.1.5 | 0.446 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3b9l | AZZ | Serum albumin | / | 0.446 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.446 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.445 | |
| 1f28 | UMP | Thymidylate synthase | 2.1.1.45 | 0.445 | |
| 1i2c | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.445 | |
| 1ja1 | FAD | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.445 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.445 | |
| 5d5b | CAU | Beta-2 adrenergic receptor | / | 0.445 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.444 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1y56 | ATP | Uncharacterized protein | / | 0.444 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.444 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.444 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.444 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 1nja | DCM | Thymidylate synthase | / | 0.443 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.443 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.442 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.442 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.442 | |
| 2uzf | CAA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.442 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.442 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.441 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.441 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.441 | |
| 1yqj | 6NP | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.441 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.441 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.441 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.441 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.440 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.440 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.440 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.440 | |
| 3hf6 | LX0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.440 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.440 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 |