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 |
|---|---|---|---|
| 2fg5 | GNP | Ras-related protein Rab-31 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 1.000 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.552 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.550 | |
| 4tq9 | GDP | GTPase KRas | / | 0.548 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.546 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.545 | |
| 4l8g | GDP | GTPase KRas | / | 0.543 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.541 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.538 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.534 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.532 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.530 | |
| 4l9s | GDP | GTPase HRas | / | 0.530 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.527 | |
| 3tgp | GNP | GTPase HRas | / | 0.527 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.527 | |
| 4xvr | GNP | GTPase HRas | / | 0.526 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.525 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.520 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.519 | |
| 2rgg | GNP | GTPase HRas | / | 0.519 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.518 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.518 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.517 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.514 | |
| 4epx | GDP | GTPase KRas | / | 0.514 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.512 | |
| 4lpk | GDP | GTPase KRas | / | 0.512 | |
| 4obe | GDP | GTPase KRas | / | 0.512 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.510 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.509 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.508 | |
| 4q03 | GDP | GTPase KRas | / | 0.507 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.507 | |
| 4epw | GDP | GTPase KRas | / | 0.505 | |
| 4lrw | GDP | GTPase KRas | / | 0.504 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.503 | |
| 4xvq | GNP | GTPase HRas | / | 0.503 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.502 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.499 | |
| 4ql3 | GDP | GTPase KRas | / | 0.499 | |
| 4lv6 | GDP | GTPase KRas | / | 0.498 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.496 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.492 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.492 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.491 | |
| 4ldj | GDP | GTPase KRas | / | 0.491 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.490 | |
| 4wa7 | GDP | GTPase KRas | / | 0.490 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.488 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.488 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.487 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.487 | |
| 3lbh | GNP | GTPase HRas | / | 0.487 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.487 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.486 | |
| 4q02 | GDP | GTPase KRas | / | 0.486 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.484 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.484 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.483 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.482 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.482 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.482 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.481 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.481 | |
| 3ddc | GNP | GTPase HRas | / | 0.480 | |
| 3v4f | GNP | GTPase HRas | / | 0.479 | |
| 3k9l | GNP | GTPase HRas | / | 0.478 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.477 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.477 | |
| 4dsn | GCP | GTPase KRas | / | 0.477 | |
| 4xrb | NDP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.477 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.476 | |
| 2c5l | GTP | GTPase HRas | / | 0.476 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.476 | |
| 4g0n | GNP | GTPase HRas | / | 0.476 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.474 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.473 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.473 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.472 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.472 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.471 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.470 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.469 | |
| 3k8y | GNP | GTPase HRas | / | 0.469 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 2ce2 | GDP | GTPase HRas | / | 0.465 | |
| 2rgb | GNP | GTPase HRas | / | 0.465 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.465 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.464 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.464 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.463 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.463 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.463 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.463 | |
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 0.462 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.462 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.460 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.458 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.458 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.458 | |
| 4dlw | GNP | GTPase HRas | / | 0.458 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.457 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2cl6 | CAG | GTPase HRas | / | 0.457 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.457 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.456 | |
| 2rgc | GNP | GTPase HRas | / | 0.456 | |
| 2rge | GNP | GTPase HRas | / | 0.456 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.456 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.455 | |
| 3lbn | GNP | GTPase HRas | / | 0.455 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.455 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.454 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.454 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 1u33 | LM2 | Pancreatic alpha-amylase | / | 0.453 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.453 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.453 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 4f6w | 0SS | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.453 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1lfd | GNP | GTPase HRas | / | 0.452 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.452 | |
| 4dlt | GNP | GTPase HRas | / | 0.452 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.451 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.451 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.451 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.451 | |
| 3ref | GDP | Rho family GTPase | / | 0.451 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.451 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.451 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.450 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.450 | |
| 1u2o | NEC | Endoplasmin | / | 0.450 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.450 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.450 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.450 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.450 | |
| 1vjy | 460 | TGF-beta receptor type-1 | 2.7.11.30 | 0.449 | |
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.449 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.449 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.449 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3oiw | GNP | GTPase HRas | / | 0.449 | |
| 3rs4 | GNP | GTPase HRas | / | 0.449 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.449 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.448 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.448 | |
| 4mit | GTP | Rho-related protein racC | / | 0.448 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.448 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.447 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.447 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.447 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.447 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 5b2z | GNP | GTPase HRas | / | 0.446 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.446 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.445 | |
| 3rsl | GNP | GTPase HRas | / | 0.445 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.445 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.444 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2bts | U32 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3eld | SFG | Methyltransferase | / | 0.444 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.444 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.443 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.443 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.443 | |
| 3rs5 | GNP | GTPase HRas | / | 0.443 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.443 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.443 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2h2e | SA8 | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.442 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.442 | |
| 3pcg | 4HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.442 | |
| 3pcg | 4HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.442 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1vrq | FON | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3rs0 | GNP | GTPase HRas | / | 0.441 | |
| 4dlz | GNP | GTPase HRas | / | 0.441 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.441 | |
| 1a4r | GNH | Cell division control protein 42 homolog | / | 0.440 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.440 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.440 | |
| 3oiv | GNP | GTPase HRas | / | 0.440 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.440 |