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 |
|---|---|---|---|
| 4fr8 | TNG | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4fr8 | TNG | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 1.000 | |
| 3inl | BXB | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.601 | |
| 2vle | DZN | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.598 | |
| 3inj | BXB | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.581 | |
| 2y03 | 5FW | Beta-1 adrenergic receptor | / | 0.511 | |
| 4bvn | P32 | Beta-1 adrenergic receptor | / | 0.511 | |
| 1pk9 | 2FA | Purine nucleoside phosphorylase DeoD-type | / | 0.501 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.493 | |
| 1tw2 | ERT | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.486 | |
| 2pdx | ZST | Aldose reductase | 1.1.1.21 | 0.482 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.481 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.479 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.477 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.477 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.476 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.474 | |
| 3nj8 | NJ8 | Enoyl-acyl carrier reductase | / | 0.473 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.472 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.471 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.470 | |
| 3ean | NAP | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.470 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.469 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.468 | |
| 1s9d | AFB | Cytohesin-2 | / | 0.468 | |
| 1s9d | AFB | ADP-ribosylation factor 1 | / | 0.468 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.468 | |
| 3b8q | 900 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.468 | |
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.468 | |
| 3lt0 | FT1 | Enoyl-ACP reductase | / | 0.467 | |
| 5dg3 | U21 | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | / | 0.467 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.466 | |
| 1tfz | 869 | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.466 | |
| 2hzq | STR | Apolipoprotein D | / | 0.466 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.466 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.465 | |
| 3hxf | BD9 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.465 | |
| 4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.465 | |
| 1vrq | FON | Subunit alpha of sarocosine oxidase | / | 0.464 | |
| 3tub | FPU | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.464 | |
| 4u95 | MIY | Multidrug efflux pump subunit AcrB | / | 0.464 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.463 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.463 | |
| 3vnt | 0JA | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.463 | |
| 4jvm | XDI | Estrogen sulfotransferase | 2.8.2.4 | 0.463 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.462 | |
| 2zju | IM4 | Acetylcholine-binding protein | / | 0.462 | |
| 3il4 | ACO | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.462 | |
| 2fmn | 4HF | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.461 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.461 | |
| 5a8e | XTK | Beta-1 adrenergic receptor | / | 0.461 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.460 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.459 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.458 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.457 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.457 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.457 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 1e1f | PSG | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.456 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.456 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 3wip | ACH | Acetylcholine-binding protein | / | 0.456 | |
| 5d0r | B1T | Adenylate cyclase type 10 | / | 0.456 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.455 | |
| 1pr1 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.455 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2z4w | 749 | Geranylgeranyl pyrophosphate synthase | / | 0.455 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.455 | |
| 2r0g | 7CK | Putative FAD-monooxygenase | / | 0.454 | |
| 3ele | PLP | Aminotransferase | / | 0.454 | |
| 4jnc | 1LF | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.454 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.454 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 1re0 | AFB | ADP-ribosylation factor 1 | / | 0.453 | |
| 1re0 | AFB | ARF guanine-nucleotide exchange factor 1 | / | 0.453 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2xnn | 430 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.453 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.453 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 2q5q | KPV | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.452 | |
| 3mb9 | ZST | Aldose reductase | 1.1.1.21 | 0.452 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.452 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4k4e | K4E | Tankyrase-1 | 2.4.2.30 | 0.452 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.451 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.451 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.451 | |
| 3dlg | GWE | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 4iae | 1DX | Alr2278 protein | / | 0.451 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.451 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.450 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.450 | |
| 3lt1 | FT2 | Enoyl-ACP reductase | / | 0.450 | |
| 1g3m | PCQ | Estrogen sulfotransferase | 2.8.2.4 | 0.449 | |
| 1pj6 | FOL | Dimethylglycine oxidase | 1.5.3.10 | 0.449 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2zd1 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 3eku | CY9 | Actin-5C | / | 0.449 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3u3o | 3QV | Sulfotransferase 1A1 | 2.8.2.1 | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.449 | |
| 4jvn | YUG | Estrogen sulfotransferase | 2.8.2.4 | 0.449 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 1pg0 | MOD | Methionine--tRNA ligase | 6.1.1.10 | 0.448 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2b04 | CHO | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.448 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 2dv0 | ZST | Aldose reductase | 1.1.1.21 | 0.448 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.448 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.448 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.447 | |
| 2x23 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.447 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 3hzi | ATP | Serine/threonine-protein kinase toxin HipA | / | 0.447 | |
| 4dm8 | REA | Retinoic acid receptor beta | / | 0.447 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.447 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.446 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.446 | |
| 2cl5 | BIE | Catechol O-methyltransferase | 2.1.1.6 | 0.446 | |
| 2r2g | EMF | Eugenol synthase 1 | 1.1.1.318 | 0.446 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.446 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.446 | |
| 3zpq | XF5 | Beta-1 adrenergic receptor | / | 0.446 | |
| 4lsa | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.446 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.446 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.446 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 1q1g | MTI | Purine nucleoside phosphorylase | / | 0.445 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.445 | |
| 2xnv | VU3 | Soluble acetylcholine receptor | / | 0.445 | |
| 4phl | PIL | Phosphodiesterase | / | 0.445 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.444 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.444 | |
| 3g1m | RF3 | HTH-type transcriptional regulator EthR | / | 0.444 | |
| 3q0u | LL3 | HTH-type transcriptional regulator EthR | / | 0.444 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.444 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.444 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1s2c | FLF | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 1t40 | ID5 | Aldose reductase | 1.1.1.21 | 0.443 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1zz1 | SHH | Histone deacetylase-like amidohydrolase | 3.5.1 | 0.443 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.443 | |
| 2r04 | W71 | Genome polyprotein | / | 0.443 | |
| 3n39 | FMN | Protein NrdI | / | 0.443 | |
| 3ox1 | 695 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.443 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3sfi | 3SF | HTH-type transcriptional regulator EthR | / | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.443 | |
| 5a2w | AGS | Mitochondrial poly(A) polymerase | / | 0.443 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.443 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 3gfx | FMN | Uncharacterized protein | / | 0.442 | |
| 3ua1 | 08Y | Cytochrome P450 3A4 | / | 0.442 | |
| 4c2j | COA | 3-ketoacyl-CoA thiolase, mitochondrial | 2.3.1.16 | 0.442 | |
| 4dm6 | TTB | Retinoic acid receptor beta | / | 0.442 | |
| 4ha6 | PXM | Pyridoxine 4-oxidase | / | 0.442 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 4msk | 2C8 | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.442 | |
| 1egc | CO8 | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.441 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.441 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.441 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.441 | |
| 3o8g | O8G | HTH-type transcriptional regulator EthR | / | 0.441 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.440 | |
| 1e2l | TMC | Thymidine kinase | / | 0.440 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 3r9f | GSU | MccE protein | / | 0.440 | |
| 4i5v | B4P | Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2 | / | 0.440 | |
| 4qrc | 0LI | Fibroblast growth factor receptor 4 | 2.7.10.1 | 0.440 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.440 | |
| 5h84 | 1VU | Histone acetyltransferase KAT2A | 2.3.1.48 | 0.440 |