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 |
|---|---|---|---|
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 1.000 | |
| 1lrm | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.659 | |
| 1tg2 | H2B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.609 | |
| 1j8u | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.578 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.576 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.573 | |
| 4pah | LNR | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.545 | |
| 5pah | LDP | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.537 | |
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.501 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.486 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.473 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.466 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.466 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.459 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.459 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.457 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.457 | |
| 5dp2 | NAP | CurF | / | 0.456 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.455 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.455 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.454 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.453 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.451 | |
| 4j7h | TRH | PCZA361.3 | / | 0.451 | |
| 1p5r | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.449 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.448 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.447 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.447 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.447 | |
| 2po3 | T4K | 4-dehydrase | / | 0.447 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.447 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.447 | |
| 4yfy | 0FX | VioF | / | 0.447 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.446 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.446 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.445 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.444 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.444 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.443 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.443 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.442 | |
| 1qvt | PRL | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.442 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.442 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.442 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.441 | |
| 1t5b | FMN | FMN-dependent NADH-azoreductase | / | 0.441 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.441 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.440 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.440 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 |