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 |
|---|---|---|---|
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.000 | |
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.854 | |
| 1upb | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.834 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.705 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.629 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.594 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.536 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.524 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.487 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.487 | |
| 2uza | HTL | Pyruvate synthase | / | 0.487 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.483 | |
| 3eya | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.483 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.482 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.481 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.478 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.472 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.471 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.471 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.471 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.471 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.469 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.467 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.467 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.467 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.467 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.467 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.466 | |
| 2c3p | 1TP | Pyruvate synthase | / | 0.465 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.465 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.465 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.465 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.464 | |
| 4u0o | MTA | Lipoyl synthase 2 | / | 0.464 | |
| 1ovm | TPP | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.463 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.463 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.463 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.462 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.462 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.462 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.462 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.461 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.460 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1j7k | ATP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.459 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 2pda | TPP | Pyruvate synthase | / | 0.459 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.459 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.458 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.458 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.458 | |
| 4eh3 | IRG | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 4l43 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.457 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.457 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.456 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.456 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.456 | |
| 3pjc | PJC | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.456 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.456 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.455 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.455 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.455 | |
| 1kek | HTL | Pyruvate synthase | / | 0.454 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.454 | |
| 2imf | TOM | 2-hydroxychromene-2-carboxylate isomerase | 5.99.1.4 | 0.453 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.453 | |
| 4feu | 537 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.453 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.453 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.452 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.452 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.452 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.451 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.450 | |
| 1syn | F89 | Thymidylate synthase | / | 0.450 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2c3u | 2TP | Pyruvate synthase | / | 0.450 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.450 | |
| 3oom | 507 | Activin receptor type-1 | 2.7.11.30 | 0.450 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.450 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.449 | |
| 1g28 | FMN | PHY3 | / | 0.449 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.449 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.449 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.449 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.449 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.449 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.448 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.448 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.448 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.448 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 4j0s | 1H3 | Bromodomain-containing protein 4 | / | 0.448 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.448 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.447 | |
| 2bxm | IMN | Serum albumin | / | 0.447 | |
| 2i0y | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.447 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.447 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 3gb4 | D3M | DdmC | / | 0.447 | |
| 3thr | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.447 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.447 | |
| 4umx | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.446 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.446 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.446 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.446 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.446 | |
| 3oe1 | TDL | Pyruvate decarboxylase | 4.1.1.1 | 0.446 | |
| 3x0a | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.446 | |
| 3zsy | OM3 | Integrase | / | 0.446 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.446 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.446 | |
| 4fsw | HK6 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.446 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.446 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.446 | |
| 4zth | GG5 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 1bob | ACO | Histone acetyltransferase type B catalytic subunit | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.445 | |
| 1jsc | TPP | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.445 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.445 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4asy | N5Y | Glucose-1-phosphate thymidylyltransferase | / | 0.445 | |
| 4e2b | FMN | Dehydrogenase | / | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.445 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.445 | |
| 5im3 | DTP | Ribonucleoside-diphosphate reductase | / | 0.445 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.444 | |
| 1um0 | FMN | Chorismate synthase | / | 0.444 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.444 | |
| 2mwg | FMN | Blue-light photoreceptor | / | 0.444 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.444 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.444 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.444 | |
| 4akn | S5B | Bromodomain-containing protein 2 | / | 0.444 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.443 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.443 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.443 | |
| 2pvj | P44 | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3ac1 | KZI | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.443 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.443 | |
| 3vha | VHA | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.443 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.443 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.443 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.442 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.442 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3bhr | THG | Thymidylate synthase | / | 0.442 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.442 | |
| 4lt6 | 3AT | Poly(A) polymerase gamma | 2.7.7.19 | 0.442 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.441 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.441 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.441 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.441 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2ydk | YDK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.441 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.441 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.441 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.441 | |
| 4l8u | 9AZ | Serum albumin | / | 0.441 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.440 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1qpd | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 2cdc | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.440 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.440 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3k3i | I46 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.440 |