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 |
|---|---|---|---|
| 4g8c | C6L | Alpha/beta hydrolase fold protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4g8c | C6L | Alpha/beta hydrolase fold protein | / | 1.000 | |
| 4g8b | HL6 | Alpha/beta hydrolase fold protein | / | 0.544 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.499 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.480 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.477 | |
| 1zdw | FLV | Prenyltransferase | / | 0.472 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.471 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.469 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.469 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.467 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.466 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.465 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.464 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.463 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.463 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.463 | |
| 3gts | D3M | DdmC | / | 0.462 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.462 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.460 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.454 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3c1o | NAP | Eugenol synthase | / | 0.452 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.452 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.450 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.450 | |
| 3b9l | AZZ | Serum albumin | / | 0.450 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.450 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.449 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.449 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.448 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.447 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.446 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.446 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.446 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.446 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2bxq | IMN | Serum albumin | / | 0.445 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2xvv | 9DN | Serum albumin | / | 0.445 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.445 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.444 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.443 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.443 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.443 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.442 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3sl8 | JN7 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1a26 | CNA | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.441 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.441 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1xng | DND | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.440 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.440 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |