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 |
|---|---|---|---|
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 1.000 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.617 | |
| 2aqb | TL6 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.611 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.603 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.581 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.581 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.570 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.563 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.561 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.560 | |
| 4jv3 | N32 | Beta-ketoacyl synthase | / | 0.558 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.555 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.554 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.534 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.534 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.532 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.510 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.489 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.484 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.476 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.472 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.470 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.467 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.467 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.467 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.464 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.464 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.463 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.462 | |
| 2wge | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.461 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.461 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.460 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.459 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 4bmp | FMN | Protein NrdI | / | 0.458 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.455 | |
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.455 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.455 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.455 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.455 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.455 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.452 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.452 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.451 | |
| 2r5n | TPP | Transketolase 1 | / | 0.451 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.451 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.451 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.450 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.450 | |
| 3ha7 | B32 | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.449 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.448 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.447 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.447 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.447 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.447 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.447 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.447 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.447 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.446 | |
| 2ejz | SAH | Diphthine synthase | / | 0.446 | |
| 4oxi | GAP | Enterobactin synthetase component F-related protein | / | 0.445 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.444 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.443 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.443 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.443 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.443 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.442 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.442 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.441 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.441 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 1sny | NAP | LD36273p | / | 0.440 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.440 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 |