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 |
|---|---|---|---|
| 3ln0 | 52B | Prostaglandin G/H synthase 2 | 1.14.99.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3ln0 | 52B | Prostaglandin G/H synthase 2 | 1.14.99.1 | 1.000 | |
| 6cox | S58 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.665 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.658 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.628 | |
| 3ln1 | CEL | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.619 | |
| 5ikr | ID8 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.602 | |
| 4fm5 | DF0 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.596 | |
| 4ph9 | IBP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.593 | |
| 3ntg | D72 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.592 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.592 | |
| 2ayl | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.591 | |
| 4cox | IMN | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.586 | |
| 4oty | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.578 | |
| 3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.577 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.566 | |
| 3n8x | NIM | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.557 | |
| 4rrx | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.545 | |
| 3n8w | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.536 | |
| 1eqg | IBP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.532 | |
| 1ht8 | 34C | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.528 | |
| 1eqh | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.523 | |
| 2oyu | IMS | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.517 | |
| 1q4g | BFL | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.508 | |
| 1osv | CHC | Bile acid receptor | / | 0.506 | |
| 4rrw | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.506 | |
| 4rrz | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.506 | |
| 3n8y | DIF | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.504 | |
| 3kk6 | CEL | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.502 | |
| 2oye | IM8 | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.500 | |
| 1ie4 | T44 | Transthyretin | / | 0.488 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.487 | |
| 3lpb | NVB | Tyrosine-protein kinase JAK2 | / | 0.483 | |
| 3n8z | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.483 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.483 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.483 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.477 | |
| 2dub | CO8 | Enoyl-CoA hydratase, mitochondrial | 4.2.1.17 | 0.476 | |
| 2qjy | SMA | Cytochrome b | / | 0.475 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.474 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.474 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.473 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.472 | |
| 2yiu | SMA | Cytochrome b | / | 0.471 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.471 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.471 | |
| 3vnt | 0JA | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.470 | |
| 2rs1 | W84 | Genome polyprotein | / | 0.469 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.469 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.468 | |
| 3vhk | BPK | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.466 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.465 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.465 | |
| 2p4i | MR9 | Angiopoietin-1 receptor | 2.7.10.1 | 0.465 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.465 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.464 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.463 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.463 | |
| 3ha8 | 5JZ | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.462 | |
| 3cyz | 9OD | Pheromone-binding protein ASP1 | / | 0.462 | |
| 4hjf | C2E | GGDEF family protein | / | 0.462 | |
| 2nvb | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.461 | |
| 5es7 | FON | Linear gramicidin synthase subunit A | / | 0.461 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.461 | |
| 1ppj | ANY | Cytochrome b | / | 0.460 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.460 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.459 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.459 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.458 | |
| 3vs0 | VS0 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.458 | |
| 4iae | 1DX | Alr2278 protein | / | 0.458 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.458 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.457 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.457 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.457 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.457 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.457 | |
| 4pd6 | URI | Nucleoside permease | / | 0.457 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.456 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.456 | |
| 5a27 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.455 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.455 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.455 | |
| 1wrl | TFP | Troponin C, slow skeletal and cardiac muscles | / | 0.454 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.454 | |
| 3wec | AUI | Cytochrome P450 | / | 0.454 | |
| 4a31 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.454 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.453 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.453 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 3b8q | 900 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.453 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 1s9e | ADB | Gag-Pol polyprotein | 2.7.7.49 | 0.452 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.452 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.452 | |
| 3iaa | TYD | CalG2 | / | 0.452 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.452 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.452 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 2qu6 | 857 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.451 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.451 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3dl9 | V2H | Vitamin D 25-hydroxylase | / | 0.451 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.451 | |
| 3cx5 | SMA | Cytochrome b | / | 0.450 | |
| 3tgu | WF3 | Cytochrome b | / | 0.450 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.450 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.450 | |
| 4lgh | 0JN | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.450 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.449 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.449 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.449 | |
| 3hng | 8ST | Vascular endothelial growth factor receptor 1 | 2.7.10.1 | 0.449 | |
| 4kao | KAO | Focal adhesion kinase 1 | 2.7.10.2 | 0.449 | |
| 2rr1 | W8R | Genome polyprotein | / | 0.448 | |
| 2ydw | WSH | Bromodomain-containing protein 2 | / | 0.448 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3lu6 | IMX | Serum albumin | / | 0.448 | |
| 4a32 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.448 | |
| 4ez7 | 2AN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.448 | |
| 3cxh | SMA | Cytochrome b | / | 0.447 | |
| 4a95 | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.447 | |
| 4oj4 | DIF | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.446 | |
| 2hek | GDP | Uncharacterized protein | / | 0.446 | |
| 3ttj | JBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.446 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.446 | |
| 4c2x | NHW | Glycylpeptide N-tetradecanoyltransferase 2 | / | 0.446 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.446 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.446 | |
| 1ezv | SMA | Cytochrome b | / | 0.445 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.445 | |
| 2ibz | SMA | Cytochrome b | / | 0.445 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.445 | |
| 2og8 | 1N8 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.445 | |
| 2wpx | ACO | Orf14 | / | 0.445 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.445 | |
| 4mzu | COA | WxcM-like protein | / | 0.445 | |
| 4xz3 | COA | Acyl-CoA synthetase (NDP forming) | / | 0.445 | |
| 1kb9 | SMA | Cytochrome b | / | 0.444 | |
| 1kt4 | RTL | Retinol-binding protein 4 | / | 0.444 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.444 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 2xir | 00J | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.444 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.444 | |
| 4b13 | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4h38 | 0YX | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 1brp | RTL | Retinol-binding protein 4 | / | 0.443 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1o1v | TCH | Gastrotropin | / | 0.443 | |
| 2vo0 | M03 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 4bkj | STI | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.443 | |
| 4c2u | ANP | DNA helicase | / | 0.443 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.443 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.443 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.442 | |
| 1hk1 | T44 | Serum albumin | / | 0.442 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.442 | |
| 2hj3 | FAD | FAD-linked sulfhydryl oxidase ERV1 | / | 0.442 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.442 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.442 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.442 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 4c8b | 0LI | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.442 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.442 | |
| 4ey2 | 0RM | Metallo-beta-lactamase type 2 | / | 0.442 | |
| 4wsq | KSA | AP2-associated protein kinase 1 | 2.7.11.1 | 0.442 | |
| 5a3c | NAD | SIR2 family protein | / | 0.442 | |
| 5ewj | QEL | NMDA glutamate receptor subunit | / | 0.442 | |
| 5ewj | QEL | Glutamate receptor ionotropic, NMDA 2B | / | 0.442 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1znq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.441 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.441 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.441 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.441 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.441 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3c4w | ATP | Rhodopsin kinase | / | 0.441 | |
| 3fnf | JPM | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.441 | |
| 3wxy | COA | Uncharacterized protein | / | 0.441 | |
| 4ase | AV9 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.441 | |
| 4l9q | 9TP | Serum albumin | / | 0.441 | |
| 4m69 | ANP | Receptor-interacting serine/threonine-protein kinase 3 | 2.7.11.1 | 0.441 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 1ppj | SMA | Cytochrome b | / | 0.440 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.440 | |
| 1yvj | 4ST | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.440 | |
| 2j5n | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.440 | |
| 2nmt | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.440 | |
| 2w4i | VGA | Glutamate racemase | / | 0.440 | |
| 2ylt | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 3glm | COO | Glutaconyl-CoA decarboxylase alpha subunit | / | 0.440 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.440 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 |