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 |
|---|---|---|---|
| 1x1r | GDP | Ras-related protein M-Ras |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1x1r | GDP | Ras-related protein M-Ras | / | 1.000 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.597 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.573 | |
| 4ql3 | GDP | GTPase KRas | / | 0.566 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.549 | |
| 4q03 | GDP | GTPase KRas | / | 0.547 | |
| 4epx | GDP | GTPase KRas | / | 0.545 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.538 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.536 | |
| 3tgp | GNP | GTPase HRas | / | 0.536 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.532 | |
| 4tq9 | GDP | GTPase KRas | / | 0.532 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.529 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.528 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.528 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.527 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.526 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.523 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.517 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.517 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.516 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.515 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.514 | |
| 4lv6 | GDP | GTPase KRas | / | 0.510 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.509 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.509 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.504 | |
| 4dlt | GNP | GTPase HRas | / | 0.503 | |
| 4lpk | GDP | GTPase KRas | / | 0.503 | |
| 4xvr | GNP | GTPase HRas | / | 0.502 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.500 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.499 | |
| 3lbh | GNP | GTPase HRas | / | 0.499 | |
| 4l9s | GDP | GTPase HRas | / | 0.499 | |
| 4q02 | GDP | GTPase KRas | / | 0.499 | |
| 2rgg | GNP | GTPase HRas | / | 0.498 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.497 | |
| 4ldj | GDP | GTPase KRas | / | 0.497 | |
| 4epw | GDP | GTPase KRas | / | 0.494 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.493 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.492 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.492 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.491 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.488 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.486 | |
| 3ddc | GNP | GTPase HRas | / | 0.486 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.484 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.484 | |
| 3lbn | GNP | GTPase HRas | / | 0.484 | |
| 4wa7 | GDP | GTPase KRas | / | 0.484 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.483 | |
| 3rs4 | GNP | GTPase HRas | / | 0.479 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.478 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.477 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.477 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.476 | |
| 2cl6 | CAG | GTPase HRas | / | 0.476 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.476 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.475 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.474 | |
| 2rge | GNP | GTPase HRas | / | 0.474 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.473 | |
| 4mit | GTP | Rho-related protein racC | / | 0.473 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.472 | |
| 2ce2 | GDP | GTPase HRas | / | 0.470 | |
| 3oiw | GNP | GTPase HRas | / | 0.470 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.470 | |
| 4obe | GDP | GTPase KRas | / | 0.470 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.469 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.467 | |
| 4dls | GNP | GTPase HRas | / | 0.467 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.464 | |
| 4xvq | GNP | GTPase HRas | / | 0.464 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.463 | |
| 2c5l | GTP | GTPase HRas | / | 0.463 | |
| 4dsn | GCP | GTPase KRas | / | 0.463 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.462 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.462 | |
| 2rgb | GNP | GTPase HRas | / | 0.462 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.462 | |
| 4dlz | GNP | GTPase HRas | / | 0.462 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.461 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.461 | |
| 3oiv | GNP | GTPase HRas | / | 0.461 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.461 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.461 | |
| 3rs7 | GNP | GTPase HRas | / | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.460 | |
| 1got | GDP | Guanine nucleotide-binding protein G(t) subunit alpha-1 | / | 0.459 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.459 | |
| 4lrw | GDP | GTPase KRas | / | 0.459 | |
| 1osv | CHC | Bile acid receptor | / | 0.458 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.458 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.458 | |
| 3lbi | GNP | GTPase HRas | / | 0.457 | |
| 1a4r | GNH | Cell division control protein 42 homolog | / | 0.456 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.456 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.455 | |
| 4g0n | GNP | GTPase HRas | / | 0.455 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.453 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.453 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.453 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.453 | |
| 3l8y | GNP | GTPase HRas | / | 0.452 | |
| 4jau | ADP | Sensor histidine kinase | / | 0.452 | |
| 3rs0 | GNP | GTPase HRas | / | 0.451 | |
| 1lfd | GNP | GTPase HRas | / | 0.450 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.450 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.450 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.450 | |
| 4xrb | NDP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.450 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.448 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.448 | |
| 4ys0 | ADP | Protein translocase subunit SecA | / | 0.448 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.448 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.447 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.447 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.446 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.446 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.446 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.445 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.444 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.444 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.444 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.444 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.443 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.443 | |
| 3qcx | 3Q2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.443 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.443 | |
| 5a2y | UTP | Mitochondrial poly(A) polymerase | / | 0.443 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.442 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.442 | |
| 3oiu | GNP | GTPase HRas | / | 0.442 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.442 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.441 | |
| 2bry | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.441 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.441 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 3k8y | GNP | GTPase HRas | / | 0.440 | |
| 3k9l | GNP | GTPase HRas | / | 0.440 | |
| 3rsl | GNP | GTPase HRas | / | 0.440 |