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 |
|---|---|---|---|
| 2bku | GTP | GTP-binding nuclear protein Ran |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 1.000 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.647 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.629 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.627 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.624 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.621 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.619 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.619 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.612 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.604 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.603 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.602 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.602 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.602 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.601 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.599 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.592 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.589 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.589 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.586 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.584 | |
| 3lbn | GNP | GTPase HRas | / | 0.583 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.580 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.579 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.578 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.576 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.570 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.569 | |
| 3rs7 | GNP | GTPase HRas | / | 0.569 | |
| 3rs5 | GNP | GTPase HRas | / | 0.565 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.564 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.564 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.563 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.562 | |
| 4dsn | GCP | GTPase KRas | / | 0.560 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.559 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.559 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.559 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.558 | |
| 3kud | GDP | GTPase HRas | / | 0.558 | |
| 2rge | GNP | GTPase HRas | / | 0.557 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.556 | |
| 3rsl | GNP | GTPase HRas | / | 0.554 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.552 | |
| 4k81 | GTP | GTPase HRas | / | 0.552 | |
| 3ddc | GNP | GTPase HRas | / | 0.550 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.550 | |
| 4dls | GNP | GTPase HRas | / | 0.550 | |
| 4nyj | GNP | GTPase HRas | / | 0.550 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.548 | |
| 4dlt | GNP | GTPase HRas | / | 0.548 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.547 | |
| 4dlz | GNP | GTPase HRas | / | 0.547 | |
| 4dlw | GNP | GTPase HRas | / | 0.546 | |
| 2rgb | GNP | GTPase HRas | / | 0.544 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.543 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.543 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.542 | |
| 2rgc | GNP | GTPase HRas | / | 0.542 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.541 | |
| 3rs0 | GNP | GTPase HRas | / | 0.539 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.538 | |
| 4mit | GTP | Rho-related protein racC | / | 0.538 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.537 | |
| 4dlv | GNP | GTPase HRas | / | 0.536 | |
| 3l8y | GNP | GTPase HRas | / | 0.535 | |
| 3i3s | GNP | GTPase HRas | / | 0.534 | |
| 4g0n | GNP | GTPase HRas | / | 0.534 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.533 | |
| 3v4f | GNP | GTPase HRas | / | 0.533 | |
| 5b2z | GNP | GTPase HRas | / | 0.532 | |
| 3oiu | GNP | GTPase HRas | / | 0.530 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.528 | |
| 4dlx | GNP | GTPase HRas | / | 0.527 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.526 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.526 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.526 | |
| 3oiv | GNP | GTPase HRas | / | 0.526 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.525 | |
| 4nyi | GNP | GTPase HRas | / | 0.525 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.524 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.524 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.523 | |
| 3rs4 | GNP | GTPase HRas | / | 0.521 | |
| 3k8y | GNP | GTPase HRas | / | 0.515 | |
| 3lbh | GNP | GTPase HRas | / | 0.514 | |
| 4dso | GSP | GTPase KRas | / | 0.512 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.511 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.510 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.509 | |
| 4l9w | GNP | GTPase HRas | / | 0.509 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.508 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.506 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.506 | |
| 2c5l | GTP | GTPase HRas | / | 0.503 | |
| 3oiw | GNP | GTPase HRas | / | 0.502 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.502 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.500 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.497 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.495 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.495 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.492 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.492 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.490 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.488 | |
| 3lbi | GNP | GTPase HRas | / | 0.486 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.485 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.484 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.481 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.479 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.478 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.477 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.476 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.474 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.474 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.474 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.473 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.472 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.472 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.472 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.465 | |
| 4epx | GDP | GTPase KRas | / | 0.465 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4obe | GDP | GTPase KRas | / | 0.463 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.462 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.461 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.461 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.461 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.460 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.459 | |
| 4ql3 | GDP | GTPase KRas | / | 0.459 | |
| 1svl | ADP | Large T antigen | 3.6.4 | 0.458 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.458 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.458 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.458 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.457 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.457 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.457 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.456 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4l8g | GDP | GTPase KRas | / | 0.456 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.455 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.454 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.453 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.452 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.452 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.452 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4ldj | GDP | GTPase KRas | / | 0.452 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.450 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.450 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4epw | GDP | GTPase KRas | / | 0.450 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.448 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.448 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.447 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.447 | |
| 2vcw | ZZA | Hematopoietic prostaglandin D synthase | / | 0.447 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.446 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.446 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.446 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.446 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.445 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.445 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 5kf1 | COA | Predicted acetyltransferase | / | 0.445 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.444 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3p9t | TCL | Repressor | / | 0.444 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.444 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.444 | |
| 4luc | GDP | GTPase KRas | / | 0.444 | |
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 0.443 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.443 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.443 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4i52 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.443 | |
| 4lv6 | GDP | GTPase KRas | / | 0.443 | |
| 4tq9 | GDP | GTPase KRas | / | 0.443 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.442 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.442 | |
| 1qs2 | NAD | Vip2Ac | / | 0.442 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.442 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.442 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.442 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.442 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4ohv | ANP | Protein clpf-1 | / | 0.442 | |
| 4q03 | GDP | GTPase KRas | / | 0.442 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.442 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.441 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.441 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.441 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.440 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.440 |