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 |
|---|---|---|---|
| 3qzy | FAD | FAD-linked sulfhydryl oxidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qzy | FAD | FAD-linked sulfhydryl oxidase | / | 1.000 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.506 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.504 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.501 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.494 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.493 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.492 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.490 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.487 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.486 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.485 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.483 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.482 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.482 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.482 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 1rp4 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.477 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.477 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.476 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.475 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.474 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.473 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.472 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 1fml | RTL | Retinol dehydratase | / | 0.467 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.467 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.466 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.466 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.466 | |
| 4iah | 1DX | Alr2278 protein | / | 0.466 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.465 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.464 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.463 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.463 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.463 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.463 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.462 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.462 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.462 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.461 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.460 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.459 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.459 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.458 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.458 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.457 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.457 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.457 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.457 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.456 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.456 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.456 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.455 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.455 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.455 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.454 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.454 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.454 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.453 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.453 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.453 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.453 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3tfn | 2CJ | Dehydrosqualene synthase | / | 0.452 | |
| 1xiu | REA | Retinoic acid receptor RXR | / | 0.451 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.451 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.451 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.450 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.450 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4alh | A9P | Bromodomain-containing protein 2 | / | 0.450 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.450 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.450 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.449 | |
| 3dge | ADP | Sensor histidine kinase | / | 0.449 | |
| 3vjc | ZGA | Squalene synthase | 2.5.1.21 | 0.449 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.449 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.448 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.448 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.448 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.448 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.447 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.447 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.447 | |
| 2axn | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | / | 0.447 | |
| 2c2a | ADP | Sensor histidine kinase | / | 0.447 | |
| 2jdv | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3gie | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.447 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.447 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.446 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.446 | |
| 2piu | DHT | Androgen receptor | / | 0.446 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.446 | |
| 4olf | HFG | Proline--tRNA ligase | 6.1.1.15 | 0.446 | |
| 5c93 | ACP | Two-component system histidine protein kinase | / | 0.446 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.446 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.445 | |
| 2q70 | DC8 | Estrogen receptor | / | 0.445 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.445 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.445 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 4jau | ADP | Sensor histidine kinase | / | 0.445 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.444 | |
| 2qe4 | JJ3 | Estrogen receptor | / | 0.444 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.444 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.444 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.444 | |
| 4g1n | NZT | Pyruvate kinase PKM | 2.7.1.40 | 0.444 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2ykb | YKB | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3vgn | FNN | Steroid Delta-isomerase | 5.3.3.1 | 0.443 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.443 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 1t13 | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | / | 0.442 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.442 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.442 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.442 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.442 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.442 | |
| 4lwb | QJ8 | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.442 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.442 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.442 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.442 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ia2 | TQ4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.441 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.441 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1xls | REA | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 1xng | DND | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 2o21 | 43B | Apoptosis regulator Bcl-2 | / | 0.441 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.441 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.441 | |
| 4d9e | LCS | D-cysteine desulfhydrase | / | 0.441 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.441 | |
| 1eio | GCH | Gastrotropin | / | 0.440 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.440 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2e07 | SAH | Diphthine synthase | / | 0.440 | |
| 2owu | SAH | Diphthine synthase | / | 0.440 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.440 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.440 | |
| 4h6p | FMN | Chromate reductase | / | 0.440 | |
| 4iw8 | KN3 | Estrogen receptor | / | 0.440 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4lb2 | DM5 | Serum albumin | / | 0.440 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.440 | |
| 4uga | Q05 | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.440 |