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 |
|---|---|---|---|
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 1.000 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.704 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.643 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.602 | |
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.595 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.588 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.563 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.557 | |
| 1a69 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.540 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.534 | |
| 1pk9 | 2FA | Purine nucleoside phosphorylase DeoD-type | / | 0.524 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.524 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.523 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.521 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.519 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.517 | |
| 2i4t | UA2 | Purine nucleoside phosphorylase, putative | / | 0.510 | |
| 1pr1 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.503 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.498 | |
| 5dp2 | NAP | CurF | / | 0.493 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.488 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.484 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.484 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.482 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.481 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.481 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.480 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.479 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.478 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.477 | |
| 3of3 | DIH | Purine nucleoside phosphorylase DeoD-type 1 | / | 0.477 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.477 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.476 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.476 | |
| 3jt4 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.475 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.473 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.472 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.471 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.470 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.470 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.469 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.468 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4iah | 1DX | Alr2278 protein | / | 0.468 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.468 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.467 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.467 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.466 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 4tta | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.464 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.462 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.461 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.460 | |
| 2ejz | SAH | Diphthine synthase | / | 0.459 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.459 | |
| 1c7o | PPG | Hemolysin | / | 0.458 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.458 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.457 | |
| 4zvm | DM2 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.457 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3e5a | VX6 | Aurora kinase A | 2.7.11.1 | 0.455 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.455 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.455 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.454 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.454 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 3nhp | HGZ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.453 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.453 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.452 | |
| 1vrq | FON | Subunit alpha of sarocosine oxidase | / | 0.452 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.452 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.452 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.452 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.452 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.451 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.451 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.451 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.450 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.450 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.450 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.450 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.449 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.449 | |
| 4z87 | GDP | Inosine-5'-monophosphate dehydrogenase | / | 0.449 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.448 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.448 | |
| 1k9s | FM2 | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.447 | |
| 1ycf | FMN | Nitric oxide reductase | 1 | 0.447 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.447 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.447 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.447 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.447 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.447 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.447 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3ox3 | 4X4 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.446 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 4fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.445 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.445 | |
| 3phc | IM5 | Purine nucleoside phosphorylase | / | 0.445 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 4iae | 1DX | Alr2278 protein | / | 0.445 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.445 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.445 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.444 | |
| 4phl | PIL | Phosphodiesterase | / | 0.444 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.443 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.443 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.443 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.443 | |
| 3klb | FMN | Uncharacterized protein | / | 0.443 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.442 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.442 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.442 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.442 | |
| 4o2z | 046 | Mitogen-activated protein kinase | / | 0.442 | |
| 1v48 | HA1 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.441 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.441 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.441 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.441 | |
| 4a4l | 939 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.441 | |
| 4isf | 1FX | Glucokinase | 2.7.1.2 | 0.441 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.441 | |
| 5d5a | CAU | Beta-2 adrenergic receptor | / | 0.441 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.440 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3nwl | NDP | Catalase | 1.11.1.6 | 0.440 | |
| 3six | GDP | Nodulation protein Z | / | 0.440 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4e2y | JHZ | Methyltransferase | / | 0.440 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4k4e | K4E | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.440 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.440 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.440 |