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 |
|---|---|---|---|
| 2zrf | DTP | Protein RecA |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zrf | DTP | Protein RecA | / | 1.000 | |
| 2zro | ADP | Protein RecA | / | 0.645 | |
| 2zre | AGS | Protein RecA | / | 0.618 | |
| 2zrj | AGS | Protein RecA | / | 0.612 | |
| 1xp8 | AGS | Protein RecA | / | 0.561 | |
| 2zr9 | DTP | Protein RecA | / | 0.498 | |
| 2fgj | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.487 | |
| 1xmv | ADP | Protein RecA | / | 0.478 | |
| 3ieu | GDP | GTPase Era | / | 0.475 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.468 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.467 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.467 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.467 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.466 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.463 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.461 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.460 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.460 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.458 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.457 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.456 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.456 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.455 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4mk9 | 28R | Genome polyprotein | 2.7.7.48 | 0.454 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.453 | |
| 4die | C5P | Cytidylate kinase | / | 0.453 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.452 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.451 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.450 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.449 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.449 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.447 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.447 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.447 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.446 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.445 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.445 | |
| 4l8u | 9AZ | Serum albumin | / | 0.445 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.445 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.444 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.444 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.443 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.443 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.442 | |
| 2cb3 | MLD | Peptidoglycan-recognition protein LE | / | 0.442 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.441 | |
| 1gc5 | ADP | ADP-dependent glucokinase | 2.7.1.147 | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 3pww | ROC | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.441 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.441 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.440 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 |