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 |
|---|---|---|---|
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 1.000 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.659 | |
| 4gtt | 7TQ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.631 | |
| 3hxf | BD9 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.626 | |
| 3pz3 | PZ3 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.603 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.596 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.588 | |
| 3c72 | CX1 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.568 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.555 | |
| 3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.543 | |
| 4h6p | FMN | Chromate reductase | / | 0.488 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.474 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1s36 | CEI | Obelin | / | 0.465 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.463 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.462 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.461 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.461 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.459 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.454 | |
| 4y0k | NAP | AntE | / | 0.454 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.452 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.451 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.451 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.450 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.450 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 4xwt | U5P | Ribonuclease J | / | 0.449 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.448 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.448 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.448 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1mlz | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.446 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.446 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4y1b | NAP | AntE | / | 0.446 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.445 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3rl4 | 5GP | Metallophosphoesterase MPPED2 | 3.1 | 0.445 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.443 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.442 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.442 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.441 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4ikz | AFS | Di-tripeptide ABC transporter (Permease) | / | 0.441 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |