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 |
|---|---|---|---|
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 1.000 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.615 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.603 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.589 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.587 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.578 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.564 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.562 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.559 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.558 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.552 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.546 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.545 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.545 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.543 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.539 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.536 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.536 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.533 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.531 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.529 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.528 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.523 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.522 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.519 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.514 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.513 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.513 | |
| 4nyj | GNP | GTPase HRas | / | 0.511 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.510 | |
| 3lbn | GNP | GTPase HRas | / | 0.509 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.508 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.508 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.506 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.506 | |
| 3v4f | GNP | GTPase HRas | / | 0.505 | |
| 4mit | GTP | Rho-related protein racC | / | 0.502 | |
| 4nyi | GNP | GTPase HRas | / | 0.502 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.501 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.501 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.499 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.497 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.495 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.493 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.492 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.492 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.491 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.490 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.489 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.489 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.488 | |
| 4dlt | GNP | GTPase HRas | / | 0.488 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.488 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.486 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.486 | |
| 3oiu | GNP | GTPase HRas | / | 0.484 | |
| 4dlw | GNP | GTPase HRas | / | 0.483 | |
| 4dso | GSP | GTPase KRas | / | 0.483 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.482 | |
| 2cl6 | CAG | GTPase HRas | / | 0.482 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.481 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.481 | |
| 3oiv | GNP | GTPase HRas | / | 0.479 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.477 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.474 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.473 | |
| 3rs5 | GNP | GTPase HRas | / | 0.473 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.473 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.471 | |
| 1hk4 | T44 | Serum albumin | / | 0.470 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.470 | |
| 5b2z | GNP | GTPase HRas | / | 0.466 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.465 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.465 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.463 | |
| 3rs7 | GNP | GTPase HRas | / | 0.463 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.462 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.461 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.461 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.460 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.460 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.459 | |
| 3i3s | GNP | GTPase HRas | / | 0.459 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.458 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.458 | |
| 2rew | REW | Peroxisome proliferator-activated receptor alpha | / | 0.458 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.458 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.457 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.457 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.456 | |
| 3tgp | GNP | GTPase HRas | / | 0.456 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.456 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 4dsu | GDP | GTPase KRas | / | 0.455 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.455 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1aqv | 0HG | Glutathione S-transferase P | 2.5.1.18 | 0.454 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.454 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3kud | GDP | GTPase HRas | / | 0.454 | |
| 3sii | A1R | Uncharacterized protein | / | 0.454 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.454 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.454 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.453 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.453 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.453 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.453 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.452 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.452 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1d6h | COA | Chalcone synthase 2 | 2.3.1.74 | 0.451 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.451 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.451 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.451 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1flm | FMN | FMN-binding protein | / | 0.450 | |
| 2ejz | SAH | Diphthine synthase | / | 0.450 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.450 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.450 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.450 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.449 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.449 | |
| 3a20 | FMN | FMN-binding protein | / | 0.449 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.449 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.448 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.448 | |
| 4xvr | GNP | GTPase HRas | / | 0.448 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.448 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 2emr | SAH | Diphthine synthase | / | 0.447 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1akw | FMN | Flavodoxin | / | 0.446 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 1jla | TNK | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 1lfd | GNP | GTPase HRas | / | 0.446 | |
| 1lwl | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.446 | |
| 2c9e | PID | Peridinin-chlorophyll a protein, high-salt form | / | 0.446 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.446 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.446 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.446 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.446 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.446 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.445 | |
| 1iep | STI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.445 | |
| 2d1c | NAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.445 | |
| 3dgq | EAA | Glutathione S-transferase P | 2.5.1.18 | 0.445 | |
| 3e8x | NAP | BH1520 protein | / | 0.445 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.445 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.445 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.445 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.444 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4n1g | CEI | Obelin | / | 0.444 | |
| 4phl | PIL | Phosphodiesterase | / | 0.444 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 3r7c | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.443 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.443 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.442 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3nax | MP7 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 3pch | CHB | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.442 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.441 | |
| 3eku | CY9 | Actin-5C | / | 0.441 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4dvg | GSP | Rho family GTPase | / | 0.441 | |
| 4fdp | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.440 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.440 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.440 |