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 |
|---|---|---|---|
| 4jbx | SK7 | Thymidine kinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4jbx | SK7 | Thymidine kinase | / | 1.000 | |
| 1e2j | THM | Thymidine kinase | / | 0.601 | |
| 1e2n | RCA | Thymidine kinase | / | 0.597 | |
| 4ivr | N50 | Thymidine kinase | / | 0.574 | |
| 4ivq | I43 | Thymidine kinase | / | 0.568 | |
| 1e2l | TMC | Thymidine kinase | / | 0.549 | |
| 3vtk | ADP | Thymidine kinase | / | 0.518 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.497 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.492 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.491 | |
| 4jq2 | SUZ | Aldo-keto reductase family 1 member C2 | / | 0.491 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.481 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.476 | |
| 3vri | 1KX | HLA class I histocompatibility antigen, B-57 alpha chain | / | 0.476 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.475 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.473 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.473 | |
| 3ldo | ANP | 78 kDa glucose-regulated protein | / | 0.472 | |
| 4yao | 2AM | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 1clq | GDP | DNA-directed DNA polymerase | / | 0.471 | |
| 2vqs | BVD | Deoxynucleoside kinase | / | 0.471 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.470 | |
| 2r8o | T5X | Transketolase 1 | / | 0.470 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.470 | |
| 2pa7 | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.467 | |
| 5epe | SAH | Uncharacterized protein | / | 0.466 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.465 | |
| 2c97 | JCL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.464 | |
| 2r8p | T6F | Transketolase 1 | / | 0.464 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.464 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.464 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.463 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.463 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.463 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.463 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.463 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.462 | |
| 1ih7 | GMP | DNA-directed DNA polymerase | / | 0.461 | |
| 2pam | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.461 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.461 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.460 | |
| 2v8p | CDP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.460 | |
| 3qh2 | 3NM | Thiazole tautomerase | / | 0.460 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.459 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.458 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.458 | |
| 3rdq | DTB | Streptavidin | / | 0.458 | |
| 4bqy | FNT | Egl nine homolog 1 | / | 0.458 | |
| 4f70 | 0ST | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.458 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.457 | |
| 5cns | DAT | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.457 | |
| 1qin | GIP | Lactoylglutathione lyase | 4.4.1.5 | 0.456 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.456 | |
| 3dcs | MZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.456 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.455 | |
| 1mdr | APG | Mandelate racemase | / | 0.454 | |
| 2y67 | N21 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.454 | |
| 3lq2 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.454 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.454 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.454 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.454 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 4j3m | AJ8 | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 4ju4 | 1O3 | Genome polyprotein | 2.7.7.48 | 0.453 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.453 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.452 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.452 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.452 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.452 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.452 | |
| 1hlk | 113 | Metallo-beta-lactamase type 2 | / | 0.451 | |
| 1lcw | SHM | Streptavidin | / | 0.451 | |
| 1qy2 | IPZ | Major urinary protein 1 | / | 0.451 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3myt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.451 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 3wyq | BTN | Streptavidin | / | 0.451 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.450 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.450 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.450 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.450 | |
| 3hku | TOR | Carbonic anhydrase 2 | 4.2.1.1 | 0.450 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.450 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.450 | |
| 1xh4 | R69 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.449 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 4l1x | STR | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.449 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.448 | |
| 3i6r | J5Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.448 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3tyd | XHP | Dihydropteroate synthase | / | 0.448 | |
| 4mzu | TYD | WxcM-like protein | / | 0.448 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.447 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.447 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.447 | |
| 3h23 | B54 | Dihydropteroate synthase | / | 0.447 | |
| 3o9p | MHI | Periplasmic murein peptide-binding protein | / | 0.447 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.447 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.447 | |
| 1nc1 | MTH | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | 3.2.2.9 | 0.446 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1sre | HAB | Streptavidin | / | 0.446 | |
| 1wnz | 2VA | Isoleucine--tRNA ligase | 6.1.1.5 | 0.446 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 3c3e | FO1 | 2-phospho-L-lactate transferase | / | 0.446 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.446 | |
| 4bqw | QNM | Egl nine homolog 1 | / | 0.446 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.446 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.446 | |
| 1cjv | DAD | Adenylate cyclase type 2 | / | 0.445 | |
| 1cjv | DAD | Adenylate cyclase type 5 | / | 0.445 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.445 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.445 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 5d3f | FSC | 14-3-3 protein zeta/delta | / | 0.445 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.444 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.444 | |
| 1wdk | ACO | 3-ketoacyl-CoA thiolase | / | 0.444 | |
| 1wm1 | PTB | Proline iminopeptidase | 3.4.11.5 | 0.444 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.444 | |
| 2izh | BTN | Streptavidin | / | 0.444 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 4hki | FLN | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.444 | |
| 1g8o | U5P | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.443 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.443 | |
| 2o12 | FMN | Chorismate synthase | / | 0.443 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.443 | |
| 4rp8 | ASC | Ascorbate-specific PTS system EIIC component | / | 0.443 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.443 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.443 | |
| 1mc0 | PCG | cGMP-dependent 3',5'-cyclic phosphodiesterase | / | 0.442 | |
| 1wxj | IPL | Tryptophan synthase alpha chain | / | 0.442 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2rgx | AP5 | Adenylate kinase | / | 0.442 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.442 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.442 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.442 | |
| 3pcn | DHY | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.442 | |
| 3pcn | DHY | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.442 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.441 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.441 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.441 | |
| 1rfu | PLP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2pak | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.441 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 3fu5 | 492 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.441 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.441 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.441 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.441 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.441 | |
| 4l9q | 9TP | Serum albumin | / | 0.441 | |
| 4mry | CEI | Obelin | / | 0.441 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.440 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.440 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.440 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.440 | |
| 1xh6 | R94 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2f2s | COA | Acetyl-CoA acetyltransferase, mitochondrial | 2.3.1.9 | 0.440 | |
| 2g72 | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.440 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.440 | |
| 2v95 | HCY | Corticosteroid-binding globulin | / | 0.440 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3fuf | BES | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.440 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.440 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.440 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.440 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.440 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.440 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.440 | |
| 4p5f | AR6 | Inosine-uridine nucleoside N-ribohydrolase | / | 0.440 |