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 |
|---|---|---|---|
| 2q3f | GNP | Ras-related GTP-binding protein D |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 1.000 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.528 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.526 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.520 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.514 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.513 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.513 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.512 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.510 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.502 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.498 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.497 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.496 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.494 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.493 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.493 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.493 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.492 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.491 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.491 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.485 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.483 | |
| 3tgp | GNP | GTPase HRas | / | 0.483 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.482 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.481 | |
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 0.481 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.476 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.475 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.475 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.474 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.474 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.474 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 4ylg | GDP | ADP-ribosylation factor 1, putative | / | 0.473 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.472 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.472 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.471 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.469 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.469 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.469 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.469 | |
| 4die | C5P | Cytidylate kinase | / | 0.469 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.469 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.468 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.467 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.466 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.466 | |
| 3s2v | 3HU | Glutamate receptor ionotropic, kainate 1 | / | 0.466 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.466 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.465 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.464 | |
| 3r9x | GNP | GTPase Era | / | 0.464 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.463 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.462 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.462 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.461 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.461 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.461 | |
| 1efa | NPF | Lactose operon repressor | / | 0.460 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.460 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.460 | |
| 2r9e | SDX | Citrate synthase | 2.3.3.16 | 0.460 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.459 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.459 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.459 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.458 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 4nxx | GDP | Mitochondrial dynamics protein MID51 | / | 0.458 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.457 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.457 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2rgg | GNP | GTPase HRas | / | 0.456 | |
| 3kjg | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.456 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.455 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.455 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.455 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.455 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 4giu | 636 | Anthranilate phosphoribosyltransferase | / | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.453 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.453 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 4blr | UTP | NTPase P4 | / | 0.453 | |
| 4e03 | ADP | Plasmid partitioning protein ParF | / | 0.453 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.452 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.452 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.452 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.452 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.452 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.451 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.451 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.451 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.451 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.450 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.450 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.450 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.450 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.449 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.449 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.449 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.449 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.449 | |
| 4h1v | GNP | Dynamin-1-like protein | 3.6.5.5 | 0.449 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.448 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.448 | |
| 3ref | GDP | Rho family GTPase | / | 0.448 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.448 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.448 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4lpk | GDP | GTPase KRas | / | 0.448 | |
| 4v02 | ATP | Site-determining protein | / | 0.448 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.447 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.447 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.447 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.447 | |
| 4xvq | GNP | GTPase HRas | / | 0.447 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.446 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.446 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.446 | |
| 3cwq | ADP | ParA family chromosome partitioning protein | / | 0.446 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.446 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3k8y | GNP | GTPase HRas | / | 0.446 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.446 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.445 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.445 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.445 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.445 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.445 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.445 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.445 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 3a37 | ADP | ATPase GET3 | / | 0.444 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.443 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.443 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.443 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.443 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.442 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.442 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.442 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.442 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4mkg | AP5 | Adenylate kinase | / | 0.442 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.441 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.441 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.441 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.441 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.441 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.441 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.441 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.440 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.440 | |
| 1n1e | NDE | Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal | 1.1.1.8 | 0.440 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1ydr | IQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.440 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.440 | |
| 4f6w | 0SS | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.440 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 5fdg | 0N8 | Polymerase acidic protein | / | 0.440 |