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 |
|---|---|---|---|
| 3rsl | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3rsl | GNP | GTPase HRas | / | 1.000 | |
| 2rgb | GNP | GTPase HRas | / | 0.778 | |
| 4dlw | GNP | GTPase HRas | / | 0.768 | |
| 4dlz | GNP | GTPase HRas | / | 0.768 | |
| 2rgc | GNP | GTPase HRas | / | 0.749 | |
| 3rs0 | GNP | GTPase HRas | / | 0.734 | |
| 4dlv | GNP | GTPase HRas | / | 0.732 | |
| 4dlx | GNP | GTPase HRas | / | 0.730 | |
| 3rs7 | GNP | GTPase HRas | / | 0.728 | |
| 4dlt | GNP | GTPase HRas | / | 0.704 | |
| 3lbn | GNP | GTPase HRas | / | 0.689 | |
| 4g0n | GNP | GTPase HRas | / | 0.689 | |
| 3v4f | GNP | GTPase HRas | / | 0.685 | |
| 3l8y | GNP | GTPase HRas | / | 0.667 | |
| 3rs5 | GNP | GTPase HRas | / | 0.660 | |
| 3ddc | GNP | GTPase HRas | / | 0.658 | |
| 2rge | GNP | GTPase HRas | / | 0.657 | |
| 3lbh | GNP | GTPase HRas | / | 0.657 | |
| 3rs4 | GNP | GTPase HRas | / | 0.651 | |
| 4dls | GNP | GTPase HRas | / | 0.647 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.642 | |
| 5b2z | GNP | GTPase HRas | / | 0.641 | |
| 2c5l | GTP | GTPase HRas | / | 0.639 | |
| 3i3s | GNP | GTPase HRas | / | 0.638 | |
| 4l9w | GNP | GTPase HRas | / | 0.635 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.634 | |
| 3oiw | GNP | GTPase HRas | / | 0.632 | |
| 3k8y | GNP | GTPase HRas | / | 0.631 | |
| 3oiv | GNP | GTPase HRas | / | 0.627 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.625 | |
| 3oiu | GNP | GTPase HRas | / | 0.623 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.623 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.619 | |
| 3kud | GDP | GTPase HRas | / | 0.617 | |
| 3lbi | GNP | GTPase HRas | / | 0.613 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.613 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.611 | |
| 4dsn | GCP | GTPase KRas | / | 0.607 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.606 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.606 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.605 | |
| 4l9s | GDP | GTPase HRas | / | 0.602 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.595 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.595 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.592 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.591 | |
| 4nyi | GNP | GTPase HRas | / | 0.590 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.582 | |
| 4nyj | GNP | GTPase HRas | / | 0.582 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.581 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.580 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.577 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.575 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.572 | |
| 4mit | GTP | Rho-related protein racC | / | 0.572 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.569 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.569 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.568 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.566 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.562 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.556 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.556 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.556 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.555 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.555 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.554 | |
| 4ql3 | GDP | GTPase KRas | / | 0.554 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.552 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.551 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.548 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.544 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.544 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.541 | |
| 4dso | GSP | GTPase KRas | / | 0.541 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.540 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.539 | |
| 4obe | GDP | GTPase KRas | / | 0.538 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.537 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.536 | |
| 4epx | GDP | GTPase KRas | / | 0.536 | |
| 4q03 | GDP | GTPase KRas | / | 0.536 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.534 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.533 | |
| 4epw | GDP | GTPase KRas | / | 0.533 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.531 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.530 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.528 | |
| 4tq9 | GDP | GTPase KRas | / | 0.528 | |
| 4ldj | GDP | GTPase KRas | / | 0.527 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.525 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.525 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.523 | |
| 3tgp | GNP | GTPase HRas | / | 0.522 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.519 | |
| 4wa7 | GDP | GTPase KRas | / | 0.519 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.518 | |
| 4lv6 | GDP | GTPase KRas | / | 0.518 | |
| 2ce2 | GDP | GTPase HRas | / | 0.515 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.512 | |
| 4q02 | GDP | GTPase KRas | / | 0.511 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.509 | |
| 4lpk | GDP | GTPase KRas | / | 0.509 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.508 | |
| 4xvr | GNP | GTPase HRas | / | 0.505 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.504 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.504 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.501 | |
| 4l8g | GDP | GTPase KRas | / | 0.501 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.500 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.500 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.499 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.495 | |
| 4xvq | GNP | GTPase HRas | / | 0.495 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.494 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.493 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.490 | |
| 1lfd | GNP | GTPase HRas | / | 0.490 | |
| 2rgg | GNP | GTPase HRas | / | 0.489 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.489 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.486 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.486 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.485 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.483 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.482 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.481 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.480 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.479 | |
| 3sfx | JAN | Uncharacterized protein | / | 0.479 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.478 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.477 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.477 | |
| 4lrw | GDP | GTPase KRas | / | 0.476 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.474 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.474 | |
| 3gya | COA | GCN5-related N-acetyltransferase | / | 0.472 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.470 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.470 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.469 | |
| 3tba | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.469 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.469 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.469 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.468 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.467 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.466 | |
| 3gy9 | COA | GCN5-related N-acetyltransferase | / | 0.464 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.463 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.463 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.463 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.462 | |
| 1n5t | OAL | ActVA 6 protein | / | 0.461 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.461 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.461 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.459 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.459 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.459 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.458 | |
| 2xkf | BX1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.458 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.458 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.458 | |
| 4ai8 | DZA | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.457 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.456 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.456 | |
| 4ykl | GMP | Aprataxin-like protein | 3 | 0.456 | |
| 5kf1 | COA | Predicted acetyltransferase | / | 0.456 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.455 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.455 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.454 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.454 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.454 | |
| 3up0 | D7S | aceDAF-12 | / | 0.454 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.454 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.453 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.453 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.453 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.453 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.453 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.452 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.452 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.451 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.451 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.451 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.451 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 2bxq | IMN | Serum albumin | / | 0.450 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.450 | |
| 2xvw | 9NR | Serum albumin | / | 0.449 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.449 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.449 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.449 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.448 | |
| 4k38 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.448 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.448 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.447 | |
| 5li5 | THR_ALA_ASN_PRO_SEP | KLTH0G14146p | / | 0.447 | |
| 1l8a | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.446 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.446 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.446 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.446 | |
| 1cju | FOK | Adenylate cyclase type 2 | / | 0.445 | |
| 1cju | FOK | Adenylate cyclase type 5 | / | 0.445 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.445 | |
| 2pak | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.445 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.445 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 4y6u | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.445 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 1gve | NAP | Aflatoxin B1 aldehyde reductase member 3 | 1 | 0.444 | |
| 2cl6 | CAG | GTPase HRas | / | 0.444 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.444 | |
| 2xk4 | OL2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.443 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.443 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.443 | |
| 4lb2 | DM5 | Serum albumin | / | 0.443 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.442 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.442 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.442 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4rtb | SAM | Putative thiazole biosynthesis protein ThiH | / | 0.442 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.442 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 1u0h | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1u0h | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.441 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.441 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.440 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.440 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.440 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.440 |