sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1x1r | GDP | Ras-related protein M-Ras |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1x1r | GDP | Ras-related protein M-Ras | / | 1.000 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.607 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.583 | |
| 4ql3 | GDP | GTPase KRas | / | 0.576 | |
| 4luc | GDP | GTPase KRas | / | 0.562 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.559 | |
| 4q03 | GDP | GTPase KRas | / | 0.557 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.556 | |
| 4epx | GDP | GTPase KRas | / | 0.556 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.548 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.547 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.546 | |
| 3tgp | GNP | GTPase HRas | / | 0.545 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.542 | |
| 4tq9 | GDP | GTPase KRas | / | 0.541 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.540 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.540 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.539 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.537 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.533 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.531 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.528 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.528 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.524 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.524 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.523 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.521 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.519 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.519 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.518 | |
| 4lv6 | GDP | GTPase KRas | / | 0.515 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.514 | |
| 4lpk | GDP | GTPase KRas | / | 0.512 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.511 | |
| 4xvr | GNP | GTPase HRas | / | 0.510 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.509 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.509 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.509 | |
| 4l9s | GDP | GTPase HRas | / | 0.509 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.508 | |
| 3lbh | GNP | GTPase HRas | / | 0.508 | |
| 4q02 | GDP | GTPase KRas | / | 0.508 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.507 | |
| 2rgg | GNP | GTPase HRas | / | 0.506 | |
| 4ldj | GDP | GTPase KRas | / | 0.506 | |
| 4epw | GDP | GTPase KRas | / | 0.503 | |
| 4dlt | GNP | GTPase HRas | / | 0.502 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.502 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.501 | |
| 3lbn | GNP | GTPase HRas | / | 0.501 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.501 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.500 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.497 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.495 | |
| 4wa7 | GDP | GTPase KRas | / | 0.493 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.492 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.492 | |
| 3ddc | GNP | GTPase HRas | / | 0.492 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.491 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.491 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.490 | |
| 3i3s | GNP | GTPase HRas | / | 0.490 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.490 | |
| 2cl6 | CAG | GTPase HRas | / | 0.489 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.488 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.488 | |
| 3rs4 | GNP | GTPase HRas | / | 0.488 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.486 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.483 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.483 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.482 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.481 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.480 | |
| 2ce2 | GDP | GTPase HRas | / | 0.479 | |
| 3oiw | GNP | GTPase HRas | / | 0.479 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.479 | |
| 4obe | GDP | GTPase KRas | / | 0.479 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.478 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.477 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.477 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.477 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.476 | |
| 4dls | GNP | GTPase HRas | / | 0.476 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.474 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.473 | |
| 2c5l | GTP | GTPase HRas | / | 0.472 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.472 | |
| 3rs7 | GNP | GTPase HRas | / | 0.472 | |
| 4dsn | GCP | GTPase KRas | / | 0.472 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.471 | |
| 2rgb | GNP | GTPase HRas | / | 0.471 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.471 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.471 | |
| 4xvq | GNP | GTPase HRas | / | 0.471 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.470 | |
| 2rge | GNP | GTPase HRas | / | 0.470 | |
| 4dlz | GNP | GTPase HRas | / | 0.470 | |
| 4k81 | GTP | GTPase HRas | / | 0.470 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.470 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.469 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.469 | |
| 4mit | GTP | Rho-related protein racC | / | 0.469 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.469 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.468 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.468 | |
| 4lrw | GDP | GTPase KRas | / | 0.467 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.466 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.466 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.465 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.465 | |
| 3lbi | GNP | GTPase HRas | / | 0.465 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.464 | |
| 3oiv | GNP | GTPase HRas | / | 0.464 | |
| 4g0n | GNP | GTPase HRas | / | 0.464 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.464 | |
| 4ylg | GDP | ADP-ribosylation factor 1, putative | / | 0.464 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.464 | |
| 1osv | CHC | Bile acid receptor | / | 0.463 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.461 | |
| 1lfd | GNP | GTPase HRas | / | 0.461 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.461 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.461 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.460 | |
| 1onp | FOM | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.460 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.460 | |
| 3l8y | GNP | GTPase HRas | / | 0.460 | |
| 4jau | ADP | Sensor histidine kinase | / | 0.460 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.459 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.459 | |
| 3rs0 | GNP | GTPase HRas | / | 0.459 | |
| 3v4f | GNP | GTPase HRas | / | 0.459 | |
| 4dsu | GDP | GTPase KRas | / | 0.459 | |
| 1a4r | GNH | Cell division control protein 42 homolog | / | 0.458 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.457 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.457 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.457 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.456 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.456 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.456 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.456 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.456 | |
| 1got | GDP | Guanine nucleotide-binding protein G(t) subunit alpha-1 | / | 0.455 | |
| 1o04 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.455 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.455 | |
| 3oiu | GNP | GTPase HRas | / | 0.455 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.455 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.455 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.455 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.454 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.454 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.453 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.453 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.452 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.452 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.452 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.452 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 1o01 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.451 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.451 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.451 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4nyj | GNP | GTPase HRas | / | 0.451 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.450 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.450 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.450 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.450 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.450 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3k9l | GNP | GTPase HRas | / | 0.449 | |
| 3rsl | GNP | GTPase HRas | / | 0.449 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.449 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.448 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.448 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.448 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.448 | |
| 3k8y | GNP | GTPase HRas | / | 0.448 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.448 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.447 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.447 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.447 | |
| 3wag | TYD | Glycosyltransferase | / | 0.447 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.447 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.446 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.446 | |
| 2bry | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.446 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2vo4 | GTB | 2,4-D inducible glutathione S-transferase | / | 0.446 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.446 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.446 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.446 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.446 | |
| 4l8g | GDP | GTPase KRas | / | 0.446 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.445 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.445 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.445 | |
| 2rgc | GNP | GTPase HRas | / | 0.445 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.445 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.444 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.444 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.444 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.444 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.443 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1coz | CTP | Glycerol-3-phosphate cytidylyltransferase | 2.7.7.39 | 0.442 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.442 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.442 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.441 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.441 | |
| 2e48 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.441 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.441 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.441 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.441 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 5a2y | UTP | Mitochondrial poly(A) polymerase | / | 0.441 | |
| 5b2z | GNP | GTPase HRas | / | 0.441 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.441 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.440 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 1x14 | NAD | NAD(P) transhydrogenase subunit alpha | 1.6.1.2 | 0.440 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.440 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.440 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.440 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4gav | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.440 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.440 |