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 |
|---|---|---|---|
| 3tjs | D0R | Cytochrome P450 3A4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3tjs | D0R | Cytochrome P450 3A4 | / | 1.000 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.570 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.552 | |
| 3wec | AUI | Cytochrome P450 | / | 0.551 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.532 | |
| 4dvq | 1CA | Cytochrome P450 11B2, mitochondrial | 1.14.15.4 | 0.530 | |
| 2j0d | ERY | Cytochrome P450 3A4 | / | 0.528 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.526 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.525 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.523 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.521 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.520 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.518 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.509 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.500 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.498 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.496 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.495 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.492 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.492 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.491 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.486 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.486 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.486 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.485 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.483 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.482 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.482 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.482 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.482 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.482 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.476 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 4l9q | 9TP | Serum albumin | / | 0.475 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.475 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.474 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.472 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.468 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.467 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.467 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.467 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.465 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.463 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.463 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.461 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.461 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.461 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.460 | |
| 2y3s | TIR | TamL | / | 0.460 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.459 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.459 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 4a1z | ADP | Kinesin-like protein KIF11 | / | 0.459 | |
| 1owm | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.458 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.458 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.458 | |
| 2ybo | SAH | Methyltransferase | / | 0.458 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.458 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.457 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.456 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4h3y | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.456 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.455 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.455 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.454 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.452 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2w1f | L0F | Aurora kinase A | 2.7.11.1 | 0.452 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.452 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.452 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.452 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.452 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.451 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 4zca | ADP | Kinesin-like protein KIF11 | / | 0.451 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.450 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.450 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.450 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.450 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.448 | |
| 3c50 | ADP | Rhodopsin kinase | / | 0.448 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1m9r | INE | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.447 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.447 | |
| 4jlo | ADP | Adenylate kinase | / | 0.447 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.446 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.446 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.446 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.446 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.445 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.445 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.445 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.445 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.445 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.445 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.444 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.444 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.444 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.444 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.443 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.443 | |
| 1pyx | ANP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.443 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 3rdq | DTB | Streptavidin | / | 0.443 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 2y3r | TRK | TamL | / | 0.442 | |
| 3mfu | ANP | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 4a28 | ADP | Kinesin-like protein KIF11 | / | 0.442 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1t0i | FMN | NAD(P)H-dependent FMN reductase LOT6 | / | 0.441 | |
| 2bxm | IMN | Serum albumin | / | 0.441 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.441 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3lu7 | IPX | Serum albumin | / | 0.441 | |
| 4hjf | C2E | GGDEF family protein | / | 0.441 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4o0u | ADN | Aurora kinase A | 2.7.11.1 | 0.441 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.440 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 2wpx | ACO | Orf14 | / | 0.440 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.440 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.440 | |
| 3pm0 | BHF | Cytochrome P450 1B1 | / | 0.440 | |
| 3q92 | XNB | Ketohexokinase | / | 0.440 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.440 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.440 |