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 |
|---|---|---|---|
| 1zhy | CLR | Oxysterol-binding protein homolog 4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1zhy | CLR | Oxysterol-binding protein homolog 4 | / | 1.000 | |
| 1zhz | ERG | Oxysterol-binding protein homolog 4 | / | 0.603 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.482 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.480 | |
| 4iah | 1DX | Alr2278 protein | / | 0.478 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.477 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.475 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.475 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.475 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.469 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.466 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.465 | |
| 4n1g | CEI | Obelin | / | 0.465 | |
| 1jd0 | AZM | Carbonic anhydrase 12 | 4.2.1.1 | 0.464 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.463 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.462 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3i6r | J5Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.462 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.462 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.461 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.460 | |
| 3glu | LYS_VAL_MET | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.460 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.457 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.457 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.457 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.456 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.456 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.456 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.455 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.455 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.455 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.455 | |
| 4bzn | UGX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.455 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.454 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.454 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.453 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.453 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.452 | |
| 1eio | GCH | Gastrotropin | / | 0.452 | |
| 2i9p | NAD | 3-hydroxyisobutyrate dehydrogenase, mitochondrial | 1.1.1.31 | 0.452 | |
| 3eks | CY9 | Actin-5C | / | 0.452 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.451 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 1z2i | NAD | Putative malate dehydrogenase | / | 0.451 | |
| 3pfh | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.451 | |
| 3px2 | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.451 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.450 | |
| 4boe | CLR | Japanin | / | 0.450 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.450 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.450 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.449 | |
| 3c1o | NAP | Eugenol synthase | / | 0.449 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.449 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.449 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1c7o | PPG | Hemolysin | / | 0.448 | |
| 1gaq | FAD | Ferredoxin | / | 0.448 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.448 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.448 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.448 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.448 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.448 | |
| 4bzo | 676 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.448 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1y6o | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.447 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.447 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.446 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.446 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.446 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.446 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.446 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.446 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.445 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.445 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.445 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.445 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.444 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.444 | |
| 4lnb | ED5 | CaaX farnesyltransferase beta subunit Ram1 | / | 0.444 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.443 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.443 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.443 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.443 | |
| 3fw3 | ETS | Carbonic anhydrase 4 | 4.2.1.1 | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.443 | |
| 3nks | ACJ | Protoporphyrinogen oxidase | 1.3.3.4 | 0.443 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.443 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.443 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.443 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.442 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.442 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.442 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.442 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 3gx9 | TXD | Morphinone reductase | / | 0.442 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.442 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.441 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.441 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.441 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.441 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3vri | 1KX | HLA class I histocompatibility antigen, B-57 alpha chain | / | 0.441 | |
| 4iae | 1DX | Alr2278 protein | / | 0.441 | |
| 4jic | FMN | GTN Reductase | / | 0.441 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.441 | |
| 4nbb | 9CA | Terminal oxygenase component of carbazole | / | 0.441 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.441 | |
| 4rel | KMP | Glycosyltransferase | / | 0.441 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.440 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.440 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3px3 | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.440 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.440 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.440 |