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 |
|---|---|---|---|
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 1.000 | |
| 3cx6 | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.579 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.528 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.516 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.514 | |
| 3cx8 | GSP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.502 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.501 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.495 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.491 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.488 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.483 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.475 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.473 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.473 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.472 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.472 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.471 | |
| 3up0 | D7S | aceDAF-12 | / | 0.471 | |
| 1lik | ADN | Adenosine kinase | 2.7.1.20 | 0.465 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.465 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.465 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 3nuu | JOZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.462 | |
| 1hw5 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.461 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.460 | |
| 1civ | NAP | Malate dehydrogenase [NADP], chloroplastic | 1.1.1.82 | 0.459 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.459 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.459 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.457 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.457 | |
| 3qcx | 3Q2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.457 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.456 | |
| 3bhr | THG | Thymidylate synthase | / | 0.456 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.456 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.454 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.453 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.453 | |
| 3daf | FEG | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.453 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.453 | |
| 4kqw | NAP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.453 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.452 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.452 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.452 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.452 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.452 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.452 | |
| 3wsb | RWZ | Farnesyltransferase, putative | / | 0.451 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.450 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.450 | |
| 4gh2 | HK0 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.450 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.449 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.449 | |
| 3i6o | GR6 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.449 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.449 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.448 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.447 | |
| 4hxy | NDP | Plm1 | / | 0.447 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.446 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.446 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.446 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.446 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.445 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3w8q | AGS | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.445 | |
| 4fog | C2F | Thymidylate synthase ThyA | / | 0.445 | |
| 4h4y | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.445 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.444 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.444 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.444 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.444 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.444 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.444 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.444 | |
| 3b2e | ADP | ATPase GET3 | / | 0.444 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.444 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 4e07 | ACP | Plasmid partitioning protein ParF | / | 0.444 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.443 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.443 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.443 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.442 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.442 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.442 | |
| 3vob | 9PC | Cell division protein FtsZ | / | 0.442 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.442 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.441 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.441 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.441 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.441 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.440 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.440 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3dag | FEG | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.440 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4v02 | ATP | Site-determining protein | / | 0.440 |