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 |
|---|---|---|---|
| 1j8u | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1j8u | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 1.000 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.625 | |
| 5pah | LDP | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.585 | |
| 1lrm | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.580 | |
| 4pah | LNR | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.574 | |
| 1tg2 | H2B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.570 | |
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.548 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.512 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.501 | |
| 3up3 | XCA | aceDAF-12 | / | 0.480 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.479 | |
| 1zdw | FLV | Prenyltransferase | / | 0.477 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.477 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.470 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.470 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.469 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.467 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.464 | |
| 1zw9 | H64 | ATP-dependent molecular chaperone HSP82 | / | 0.464 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.464 | |
| 2vte | IK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.464 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.464 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.464 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.463 | |
| 3h18 | PMS | Esterase/lipase | / | 0.463 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.461 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.461 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.461 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3hf6 | LX0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.460 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 4xwt | U5P | Ribonuclease J | / | 0.459 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.458 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.458 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.458 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.458 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.457 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.456 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.456 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.456 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.456 | |
| 1rx6 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.455 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.454 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.454 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.454 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.454 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.454 | |
| 1fml | RTL | Retinol dehydratase | / | 0.453 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 1syn | F89 | Thymidylate synthase | / | 0.453 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.453 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.453 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.453 | |
| 4phl | PIL | Phosphodiesterase | / | 0.453 | |
| 4xp4 | COC | Sodium-dependent dopamine transporter | / | 0.453 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.452 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.451 | |
| 4dlc | UMP | Deoxyuridine triphosphatase, putative | / | 0.451 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2cje | DUN | DUTPase | / | 0.450 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2zym | ACX | Periplasmic binding protein | / | 0.450 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.449 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 2ejz | SAH | Diphthine synthase | / | 0.449 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.449 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.449 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.449 | |
| 4x2q | NAD | Retinal dehydrogenase 2 | 1.2.1.36 | 0.449 | |
| 1rzy | 5AS | Histidine triad nucleotide-binding protein 1 | 3 | 0.448 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.448 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.448 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.447 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.447 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4lt6 | 3AT | Poly(A) polymerase gamma | 2.7.7.19 | 0.447 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.447 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1bxs | NAD | Retinal dehydrogenase 1 | 1.2.1.36 | 0.446 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.446 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.446 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.446 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.446 | |
| 3w0t | HPU | Lactoylglutathione lyase | 4.4.1.5 | 0.446 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.446 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.445 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.445 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.445 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.445 | |
| 3up0 | D7S | aceDAF-12 | / | 0.445 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 3zm6 | 2GN | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.445 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1rc4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.444 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.444 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.444 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.444 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 2pak | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.443 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.443 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.443 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.443 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.442 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.442 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.442 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.442 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.442 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.442 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3iss | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.441 | |
| 3q33 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.441 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.441 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.441 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 5cho | FAD | Flavin reductase | / | 0.441 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.441 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.440 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.440 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.440 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.440 | |
| 1v79 | FR7 | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.440 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3ox3 | 4X4 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.440 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.440 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.440 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.440 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.440 |