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 |
|---|---|---|---|
| 5itz | LOC | Tubulin beta-2B chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5itz | LOC | Tubulin beta-2B chain | / | 1.000 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.619 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.580 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.538 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.495 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.494 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.489 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.489 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.488 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.487 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.479 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.479 | |
| 1hwz | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.477 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.472 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.471 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.469 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.469 | |
| 3ete | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.468 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.466 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.466 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.465 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.463 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.463 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.463 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.462 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.461 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.461 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.460 | |
| 3zuy | TCH | Transporter | / | 0.460 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.460 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.459 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.459 | |
| 3zux | TCH | Transporter | / | 0.459 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.458 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.458 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.458 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.458 | |
| 1zmd | NAI | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.457 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.457 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.457 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.456 | |
| 2c6h | PXI | Cytochrome P450 monooxygenase PikC | / | 0.456 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.456 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.455 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.454 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.454 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.454 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 1sn5 | T3 | Transthyretin | / | 0.453 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.453 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.453 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.452 | |
| 1ie4 | T44 | Transthyretin | / | 0.451 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.451 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1sn0 | T44 | Transthyretin | / | 0.450 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.450 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.450 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.450 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.449 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.449 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.449 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 1dra | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.448 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.447 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.447 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.447 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.447 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.446 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.446 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.446 | |
| 3jw3 | TOP | Dihydrofolate reductase | / | 0.446 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 1fml | RTL | Retinol dehydratase | / | 0.445 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.445 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.445 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.445 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.445 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.444 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.443 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4irn | FAD | AnaB | / | 0.443 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1rv1 | IMZ | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.442 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.442 | |
| 4l9q | 9TP | Serum albumin | / | 0.442 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.442 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.441 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.441 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.441 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.441 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.441 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.441 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.441 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.440 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.440 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.440 |