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 |
|---|---|---|---|
| 5g53 | NEC | Adenosine receptor A2a |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5g53 | NEC | Adenosine receptor A2a | / | 1.000 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.582 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.558 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.557 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.554 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.547 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.546 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.545 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.538 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.537 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.533 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.525 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.524 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.519 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.511 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.505 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.502 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.495 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.491 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.488 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.486 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.484 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.480 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.480 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.479 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.476 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.475 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.475 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.474 | |
| 3up0 | D7S | aceDAF-12 | / | 0.474 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.473 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.472 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.471 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.470 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.469 | |
| 4at4 | T6E | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.469 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.468 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.468 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.467 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.466 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.466 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.466 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.466 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.466 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.466 | |
| 3rfm | CFF | Adenosine receptor A2a | / | 0.466 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.465 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.464 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.464 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 4at5 | MUJ | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.463 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.462 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.462 | |
| 4iah | 1DX | Alr2278 protein | / | 0.462 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.461 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.461 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.461 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.460 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.460 | |
| 3gki | CLR | Niemann-Pick C1 protein | / | 0.460 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.460 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.459 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.459 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.459 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.459 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.459 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.458 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.457 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 2ofv | 242 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.457 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.457 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 4bkj | STI | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.457 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.457 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.457 | |
| 1ppj | ANY | Cytochrome b | / | 0.456 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.456 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.456 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.455 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.455 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.455 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.454 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.454 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.454 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.454 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.453 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.453 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.452 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.451 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.450 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.450 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.450 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3kqj | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.449 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.449 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.449 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.449 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.448 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.448 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.447 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.447 | |
| 2mm3 | CHO | Gastrotropin | / | 0.447 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.447 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.447 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.447 | |
| 5a3b | APR | SIR2 family protein | / | 0.447 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.446 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.446 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.446 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.445 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.445 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.445 | |
| 3mzh | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.445 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.445 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.444 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.444 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.444 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.444 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.444 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.443 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.443 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.443 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.443 | |
| 2fhk | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.443 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3n83 | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.443 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.443 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.443 | |
| 4irn | FAD | AnaB | / | 0.443 | |
| 4l9q | 9TP | Serum albumin | / | 0.443 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.442 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.442 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 3stu | DK3 | Methylketone synthase I | / | 0.442 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.442 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.442 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.441 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.441 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.441 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.441 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.441 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.440 | |
| 2fhj | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.440 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.440 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4xx0 | COA | Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial | 6.2.1.4 | 0.440 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 |