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 |
|---|---|---|---|
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 1.000 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.492 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.487 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.484 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.478 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.478 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.477 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.475 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.475 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.474 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.472 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.472 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.470 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.470 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.469 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.468 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.467 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.466 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.466 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.466 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.465 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.463 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.461 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.461 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.460 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.460 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.460 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.459 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.459 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.458 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.458 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.457 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.456 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.456 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.454 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.454 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.454 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.453 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.453 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.453 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.451 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.450 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.449 | |
| 3zuy | TCH | Transporter | / | 0.449 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.448 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.448 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.448 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.447 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1osv | CHC | Bile acid receptor | / | 0.447 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.447 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.447 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2f1k | NAP | Prephenate dehydrogenase | / | 0.446 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.446 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.446 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.446 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.446 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.446 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.445 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.445 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.445 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.445 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.445 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.445 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2xa4 | AZ5 | Tyrosine-protein kinase JAK2 | / | 0.444 | |
| 2y3s | TIR | TamL | / | 0.444 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.444 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.444 | |
| 5a3b | APR | SIR2 family protein | / | 0.444 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.443 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.443 | |
| 2y4g | TIR | TamL | / | 0.443 | |
| 3u9e | COA | Lmo1369 protein | / | 0.443 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.443 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.442 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2i40 | BLZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2y3r | TRK | TamL | / | 0.442 | |
| 3gob | HXX | DdmC | / | 0.442 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.441 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.441 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 4iae | 1DX | Alr2278 protein | / | 0.441 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.441 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.440 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.440 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.440 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.440 |