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 |
|---|---|---|---|
| 4hdo | GNP | Ras-related protein Rap-1b |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4hdo | GNP | Ras-related protein Rap-1b | / | 1.000 | |
| 3lbi | GNP | GTPase HRas | / | 0.668 | |
| 2c5l | GTP | GTPase HRas | / | 0.659 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.652 | |
| 3v4f | GNP | GTPase HRas | / | 0.651 | |
| 3l8y | GNP | GTPase HRas | / | 0.648 | |
| 4dsn | GCP | GTPase KRas | / | 0.647 | |
| 3oiw | GNP | GTPase HRas | / | 0.646 | |
| 4g0n | GNP | GTPase HRas | / | 0.645 | |
| 2rgb | GNP | GTPase HRas | / | 0.639 | |
| 5b2z | GNP | GTPase HRas | / | 0.635 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.632 | |
| 3lbn | GNP | GTPase HRas | / | 0.629 | |
| 3lbh | GNP | GTPase HRas | / | 0.628 | |
| 2rgc | GNP | GTPase HRas | / | 0.626 | |
| 4dlt | GNP | GTPase HRas | / | 0.625 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.623 | |
| 4mit | GTP | Rho-related protein racC | / | 0.620 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.619 | |
| 3rs4 | GNP | GTPase HRas | / | 0.617 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.615 | |
| 3ddc | GNP | GTPase HRas | / | 0.615 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.615 | |
| 2rge | GNP | GTPase HRas | / | 0.612 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.611 | |
| 3oiv | GNP | GTPase HRas | / | 0.611 | |
| 4dlz | GNP | GTPase HRas | / | 0.607 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.606 | |
| 3rsl | GNP | GTPase HRas | / | 0.605 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.603 | |
| 4nyj | GNP | GTPase HRas | / | 0.603 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.601 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.601 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.601 | |
| 3i3s | GNP | GTPase HRas | / | 0.600 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.600 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.598 | |
| 3k8y | GNP | GTPase HRas | / | 0.598 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.597 | |
| 3rs7 | GNP | GTPase HRas | / | 0.597 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.595 | |
| 4dlx | GNP | GTPase HRas | / | 0.593 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.593 | |
| 3kud | GDP | GTPase HRas | / | 0.590 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.586 | |
| 4dlw | GNP | GTPase HRas | / | 0.585 | |
| 4dls | GNP | GTPase HRas | / | 0.584 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.583 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.583 | |
| 3rs5 | GNP | GTPase HRas | / | 0.580 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.580 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.579 | |
| 4l9w | GNP | GTPase HRas | / | 0.578 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.576 | |
| 3rs0 | GNP | GTPase HRas | / | 0.573 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.572 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.572 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.572 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.571 | |
| 4nyi | GNP | GTPase HRas | / | 0.571 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.570 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.570 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.569 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.567 | |
| 4dlv | GNP | GTPase HRas | / | 0.567 | |
| 3tgp | GNP | GTPase HRas | / | 0.565 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.560 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.560 | |
| 4dso | GSP | GTPase KRas | / | 0.559 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.558 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.551 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.550 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.548 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.546 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.546 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.545 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.545 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.545 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.545 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.540 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.539 | |
| 4tq9 | GDP | GTPase KRas | / | 0.539 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.537 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.536 | |
| 4l9s | GDP | GTPase HRas | / | 0.536 | |
| 4lpk | GDP | GTPase KRas | / | 0.536 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.536 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.534 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.532 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.531 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.530 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.529 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.527 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.527 | |
| 2rgg | GNP | GTPase HRas | / | 0.525 | |
| 4obe | GDP | GTPase KRas | / | 0.524 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.523 | |
| 2ce2 | GDP | GTPase HRas | / | 0.520 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.519 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.517 | |
| 4ql3 | GDP | GTPase KRas | / | 0.513 | |
| 4xvr | GNP | GTPase HRas | / | 0.511 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.508 | |
| 3k9l | GNP | GTPase HRas | / | 0.506 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.505 | |
| 4epx | GDP | GTPase KRas | / | 0.504 | |
| 4luc | GDP | GTPase KRas | / | 0.503 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.501 | |
| 4q03 | GDP | GTPase KRas | / | 0.500 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.499 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.499 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.499 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.494 | |
| 1lfd | GNP | GTPase HRas | / | 0.493 | |
| 4lv6 | GDP | GTPase KRas | / | 0.493 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.493 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.492 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.488 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.487 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.486 | |
| 4lrw | GDP | GTPase KRas | / | 0.486 | |
| 4q02 | GDP | GTPase KRas | / | 0.485 | |
| 4xvq | GNP | GTPase HRas | / | 0.485 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.484 | |
| 4l8g | GDP | GTPase KRas | / | 0.484 | |
| 4wa7 | GDP | GTPase KRas | / | 0.483 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.481 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.481 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.480 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.480 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.480 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.480 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.480 | |
| 4ldj | GDP | GTPase KRas | / | 0.478 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.477 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.475 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.474 | |
| 4epw | GDP | GTPase KRas | / | 0.473 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.471 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.469 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.469 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.466 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.464 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.464 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.461 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.461 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.461 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.461 | |
| 3cx6 | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.461 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.460 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.459 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.459 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.459 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.458 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.458 | |
| 2r8p | T6F | Transketolase 1 | / | 0.458 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.458 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.458 | |
| 2r8o | T5X | Transketolase 1 | / | 0.457 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.457 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.457 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.456 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.456 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.456 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.456 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.454 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.454 | |
| 4dvg | GSP | Rho family GTPase | / | 0.453 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.452 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.452 | |
| 4buv | 16I | Tankyrase-2 | 2.4.2.30 | 0.451 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.450 | |
| 2ada | HPR | Adenosine deaminase | 3.5.4.4 | 0.450 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.449 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.449 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.449 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.448 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.447 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.447 | |
| 2fhj | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.447 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.447 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.446 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2xvv | 9DN | Serum albumin | / | 0.446 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.446 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.445 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.444 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.444 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.444 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.443 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.443 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.443 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.443 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1sez | OMN | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.442 | |
| 2bxm | IMN | Serum albumin | / | 0.442 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.442 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.442 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.442 | |
| 3dh8 | B4N | Uncharacterized protein PA1000 | / | 0.441 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.441 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.441 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.441 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.441 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.441 | |
| 4hxy | NDP | Plm1 | / | 0.441 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.440 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 |