sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4b6s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4b6s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 1.000 | |
| 3n87 | N87 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.602 | |
| 2xb9 | XNW | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.601 | |
| 2wks | CB6 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.600 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.569 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.561 | |
| 2xda | JPS | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.561 | |
| 4b6r | 3DQ | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.557 | |
| 4y9u | NAP | NADPH--cytochrome P450 reductase | / | 0.495 | |
| 2y71 | CB6 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.494 | |
| 2xb8 | XNW | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.492 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.487 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.478 | |
| 3n76 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.476 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.475 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.475 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.473 | |
| 5dp2 | NAP | CurF | / | 0.473 | |
| 2yj4 | ATP | Copper-transporting ATPase | / | 0.469 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.465 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.463 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.463 | |
| 1nqw | 5YL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.460 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4v0s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.459 | |
| 4yau | 2AM | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.457 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.457 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.457 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3n71 | SFG | Histone-lysine N-methyltransferase Smyd1 | / | 0.455 | |
| 5doz | NDP | JamJ | / | 0.454 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.453 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.452 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.452 | |
| 1qsn | COA | HAT A1 | / | 0.451 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.451 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.451 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.451 | |
| 4rph | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.451 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.449 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.449 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.449 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.448 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.447 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3gb4 | D3M | DdmC | / | 0.447 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.447 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.446 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.446 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.445 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.445 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.444 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.444 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.444 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.443 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.443 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.443 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.442 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2v5u | FMN | Flavodoxin | / | 0.442 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.442 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.441 | |
| 3v2u | ATP | Protein GAL3 | / | 0.441 | |
| 4l4x | NDP | AmphI | / | 0.441 | |
| 4qij | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.441 | |
| 4uz6 | SCR | Palmitoleoyl-protein carboxylesterase NOTUM | / | 0.441 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.440 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.440 | |
| 5iqd | GNP | Bifunctional AAC/APH | 2.3.1 | 0.440 |