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 |
|---|---|---|---|
| 1el4 | CTZ | Obelin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1el4 | CTZ | Obelin | / | 1.000 | |
| 1qv0 | CZH | Obelin | / | 0.658 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.650 | |
| 1jf2 | CZH | Obelin | / | 0.639 | |
| 1uhh | CZP | Aequorin-2 | / | 0.637 | |
| 1qv1 | CZH | Obelin | / | 0.632 | |
| 4n1f | CZH | Obelin | / | 0.631 | |
| 4nqg | CZH | Mitrocomin | / | 0.629 | |
| 1uhj | CZB | Aequorin-2 | / | 0.626 | |
| 1jf0 | CZH | Obelin | / | 0.624 | |
| 1s36 | CEI | Obelin | / | 0.605 | |
| 4mrx | CZH | Obelin | / | 0.583 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.505 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.491 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.489 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.484 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.483 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.483 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.481 | |
| 4iae | 1DX | Alr2278 protein | / | 0.481 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.480 | |
| 4n1g | CEI | Obelin | / | 0.479 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.478 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.478 | |
| 4iah | 1DX | Alr2278 protein | / | 0.478 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.477 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.474 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.473 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.472 | |
| 1sl9 | CZH | Obelin | / | 0.472 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.472 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.469 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.468 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.466 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.465 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.463 | |
| 2bxo | OPB | Serum albumin | / | 0.462 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.461 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.461 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.460 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.460 | |
| 4h7c | 10H | Aldo-keto reductase family 1 member C3 | / | 0.460 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.458 | |
| 3dr4 | G4M | GDP-perosamine synthase | / | 0.457 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.457 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.454 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.453 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.453 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.453 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.453 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3b9l | AZZ | Serum albumin | / | 0.452 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.452 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.452 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.451 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.451 | |
| 1s2c | FLF | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.451 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.450 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.448 | |
| 4hmn | 16J | Aldo-keto reductase family 1 member C3 | / | 0.448 | |
| 4qij | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.448 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.447 | |
| 2bru | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.447 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.447 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.447 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.447 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.447 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.446 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.446 | |
| 2plm | SIB | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | 3.5.4.28 | 0.446 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.446 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.446 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.445 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.445 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 5kf1 | COA | Predicted acetyltransferase | / | 0.445 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.445 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.444 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.444 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.443 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.443 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.443 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 1c7o | PPG | Hemolysin | / | 0.442 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 1xh5 | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3bt9 | DEQ | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.442 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3fnu | 006 | HAP protein | / | 0.442 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.442 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.442 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.442 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.441 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.441 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.441 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.441 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4j7g | TRH | PCZA361.3 | / | 0.441 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.440 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.440 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 5agy | GTB | Tau class glutathione S-transferase | / | 0.440 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.440 |