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 |
|---|---|---|---|
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 1.000 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.608 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.604 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.586 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.581 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.575 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.571 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.568 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.562 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.562 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.547 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.545 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.545 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.544 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.544 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.540 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.538 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.538 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.536 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.528 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.527 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.525 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.524 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.524 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.523 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.521 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.520 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.518 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.517 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.517 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.516 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.516 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.512 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.512 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.509 | |
| 4nyj | GNP | GTPase HRas | / | 0.508 | |
| 4nyi | GNP | GTPase HRas | / | 0.507 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.506 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.504 | |
| 3lbn | GNP | GTPase HRas | / | 0.502 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.500 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.499 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.498 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.496 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.496 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.492 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.492 | |
| 3v4f | GNP | GTPase HRas | / | 0.491 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.490 | |
| 4k81 | GTP | GTPase HRas | / | 0.490 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.489 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.489 | |
| 4mit | GTP | Rho-related protein racC | / | 0.489 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.489 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.487 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.487 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.487 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.487 | |
| 4dlt | GNP | GTPase HRas | / | 0.487 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.486 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.485 | |
| 3tgp | GNP | GTPase HRas | / | 0.483 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.483 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.481 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.480 | |
| 3kud | GDP | GTPase HRas | / | 0.480 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.479 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.478 | |
| 2cl6 | CAG | GTPase HRas | / | 0.477 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.477 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.475 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.474 | |
| 1lfd | GNP | GTPase HRas | / | 0.472 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.472 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.472 | |
| 3oiv | GNP | GTPase HRas | / | 0.471 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.470 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.470 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.467 | |
| 1c7o | PPG | Hemolysin | / | 0.466 | |
| 3rs5 | GNP | GTPase HRas | / | 0.466 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.466 | |
| 4ohx | ADP | Protein clpf-1 | / | 0.466 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.465 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.463 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.462 | |
| 2gd2 | CAA | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.462 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.462 | |
| 3rs7 | GNP | GTPase HRas | / | 0.462 | |
| 2rgc | GNP | GTPase HRas | / | 0.461 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.461 | |
| 2c5l | GTP | GTPase HRas | / | 0.460 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.460 | |
| 4ohv | ANP | Protein clpf-1 | / | 0.460 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.459 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 4dvg | GSP | Rho family GTPase | / | 0.459 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.458 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.458 | |
| 5bn3 | ADP | NEQ263 | / | 0.458 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.457 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.457 | |
| 2rbe | ZMG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 3oiu | GNP | GTPase HRas | / | 0.457 | |
| 4dlw | GNP | GTPase HRas | / | 0.457 | |
| 3rs0 | GNP | GTPase HRas | / | 0.456 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1hk4 | T44 | Serum albumin | / | 0.455 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.455 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.455 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.455 | |
| 4dso | GSP | GTPase KRas | / | 0.455 | |
| 4l9s | GDP | GTPase HRas | / | 0.455 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.454 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.454 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 3sii | A1R | Uncharacterized protein | / | 0.454 | |
| 4dsu | GDP | GTPase KRas | / | 0.454 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.453 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.453 | |
| 1akw | FMN | Flavodoxin | / | 0.452 | |
| 1dia | L24 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.452 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.452 | |
| 4dlv | GNP | GTPase HRas | / | 0.452 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.452 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.451 | |
| 3ddc | GNP | GTPase HRas | / | 0.451 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.451 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.451 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.450 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4epw | GDP | GTPase KRas | / | 0.450 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.449 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.449 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.448 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.448 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 3sig | AR6 | Uncharacterized protein | / | 0.448 | |
| 5cyp | GSP | Septin-9 | / | 0.448 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.448 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.447 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4dlx | GNP | GTPase HRas | / | 0.447 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.447 | |
| 2emr | SAH | Diphthine synthase | / | 0.446 | |
| 2p2q | PRX | Acetyl-coenzyme A synthetase | / | 0.446 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.446 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.446 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.446 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 5bn4 | ANP | V-type ATP synthase alpha chain | / | 0.446 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1khr | VIR | Streptogramin A acetyltransferase | 2.3.1 | 0.445 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.445 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.444 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.444 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3d8x | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.444 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.444 | |
| 3p8z | 36A | Genome polyprotein | 2.1.1.56 | 0.444 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3rs4 | GNP | GTPase HRas | / | 0.443 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.443 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.443 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.442 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2ej2 | PPE | Branched-chain amino acid aminotransferase (IlvE) | / | 0.442 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.442 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.442 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.442 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3nax | MP7 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.442 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.442 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.442 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.442 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.441 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2zrf | DTP | Protein RecA | / | 0.441 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4eh8 | IRG | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 5c93 | ACP | Two-component system histidine protein kinase | / | 0.441 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.440 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.440 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2r8v | ACO | Amino-acid acetyltransferase | / | 0.440 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3i6r | J5Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.440 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.440 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.440 | |
| 4u07 | ATP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.440 | |
| 5b2z | GNP | GTPase HRas | / | 0.440 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 |