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 |
|---|---|---|---|
| 1el4 | CTZ | Obelin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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 | |
| 1jf0 | CZH | Obelin | / | 0.624 | |
| 1qv1 | CZH | Obelin | / | 0.623 | |
| 4n1f | CZH | Obelin | / | 0.622 | |
| 4nqg | CZH | Mitrocomin | / | 0.618 | |
| 1uhj | CZB | Aequorin-2 | / | 0.615 | |
| 1s36 | CEI | Obelin | / | 0.605 | |
| 4mrx | CZH | Obelin | / | 0.583 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.493 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.488 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.485 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.483 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.481 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.481 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 4n1g | CEI | Obelin | / | 0.478 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.475 | |
| 4iae | 1DX | Alr2278 protein | / | 0.474 | |
| 4iah | 1DX | Alr2278 protein | / | 0.473 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.472 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.470 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.470 | |
| 4fl0 | PLP | Aminotransferase ALD1, chloroplastic | 2.6.1 | 0.470 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.468 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.468 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.467 | |
| 2xvv | 9DN | Serum albumin | / | 0.467 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.467 | |
| 1sl9 | CZH | Obelin | / | 0.466 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.466 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.466 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.466 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.466 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.465 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.465 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 2bxo | OPB | Serum albumin | / | 0.463 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.463 | |
| 1fml | RTL | Retinol dehydratase | / | 0.461 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.461 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.461 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 4jva | 1OR | cAMP-dependent protein kinase type II-beta regulatory subunit | / | 0.461 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.459 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.459 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.458 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.458 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.458 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.456 | |
| 3dr4 | G4M | GDP-perosamine synthase | / | 0.456 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xvw | 9NR | Serum albumin | / | 0.454 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.454 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.454 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.454 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.454 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.453 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.453 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.453 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.453 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.453 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.452 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.452 | |
| 4egn | TWO | Cytochrome P450 | / | 0.452 | |
| 2zi6 | 3D1 | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.451 | |
| 4h7c | 10H | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.451 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.450 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.450 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4hmn | 16J | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.449 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.449 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.449 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 5dp2 | NAP | CurF | / | 0.449 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.447 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.447 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.447 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.447 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.446 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3b9l | AZZ | Serum albumin | / | 0.446 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.446 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.444 | |
| 2plm | SIB | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | 3.5.4.28 | 0.444 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.444 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.444 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.443 | |
| 1rgs | CMP | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.443 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.443 | |
| 3c1o | NAP | Eugenol synthase | / | 0.443 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.443 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.443 | |
| 4oe4 | NAD | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial | 1.2.1.88 | 0.443 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.442 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3fnu | 006 | HAP protein | / | 0.442 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.442 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.441 | |
| 1kqg | HQO | Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit | / | 0.440 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.440 | |
| 1qvu | PRL | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.440 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.440 | |
| 2lbv | EB4 | Extracellular fatty acid-binding protein | / | 0.440 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.440 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.440 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.440 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.440 |