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 |
|---|---|---|---|
| 3djf | BC3 | Purine nucleoside phosphorylase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 1.000 | |
| 3iex | GMP | Purine nucleoside phosphorylase | / | 0.547 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.515 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.492 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.491 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.491 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.484 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.478 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.478 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.477 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.475 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.475 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.474 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.474 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.473 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.472 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.472 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.465 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.465 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.465 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.465 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.464 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.464 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.464 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.462 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.462 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.462 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.461 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.461 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.460 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.460 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.459 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.458 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.458 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.457 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.457 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.457 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.456 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.456 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.455 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.455 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.454 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 1qv0 | CZH | Obelin | / | 0.453 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.453 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 2xvw | 9NR | Serum albumin | / | 0.453 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.453 | |
| 1qv1 | CZH | Obelin | / | 0.452 | |
| 2bxm | IMN | Serum albumin | / | 0.452 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.451 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.451 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.450 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.450 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.449 | |
| 4lsj | LSJ | Glucocorticoid receptor | / | 0.449 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1jf0 | CZH | Obelin | / | 0.448 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.448 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.448 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.448 | |
| 2imf | TOM | 2-hydroxychromene-2-carboxylate isomerase | 5.99.1.4 | 0.448 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3gur | BYG | Glutathione S-transferase Mu 2 | 2.5.1.18 | 0.448 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.447 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.447 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.447 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3h18 | PMS | Esterase/lipase | / | 0.445 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.445 | |
| 3zxs | FAD | Deoxyribodipyrimidine photolyase-related protein | / | 0.445 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 1euy | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.444 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.444 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.443 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.443 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.443 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 1u0h | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1u0h | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.442 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4n1f | CZH | Obelin | / | 0.442 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.442 | |
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 3pz3 | PZ3 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.441 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4mbs | MRV | C-C chemokine receptor type 5 | / | 0.441 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.440 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.440 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.440 | |
| 4nv7 | COA | Arylamine N-acetyltransferase | / | 0.440 |