289 Peptide deformylase
Ligands and drugs
Aggregated over all current member domains of this group. Drug annotations come from DrugDomain; buffers and crystallization additives are excluded from the tables below.
Chemical profile
ClassyFire chemical superclasses of the ligands bound by this X-group's proteins, from DrugDomain annotations.
The raw number of superclasses rises with the number of proteins sampled; the per-20 value compares X-groups at equal depth.
| Superclass | Proteins | Expected | 0.25×observed / expected4× | Ratio | Significance |
|---|---|---|---|---|---|
| Organic acids and derivatives | 32 | 6.6 | 4.88× | q < 0.0001 | |
| Homogeneous metal compounds | 43 | 20.8 | 2.07× | q < 0.0001 | |
| Organoheterocyclic compounds | 7 | 6.5 | 1.07× | q = 0.88 | |
| Organic oxygen compounds | 8 | 8.4 | 0.95× | q = 1.00 | |
| Homogeneous non-metal compounds | 6 | 9.1 | 0.66× | q = 0.43 | |
| Nucleosides, nucleotides, and analogues | 0 | 11.7 | 0 | q < 0.0001 | |
| Benzenoids | 7 | 3.1 | 2.26× | not tested | |
| Organosulfur compounds | 1 | 0.9 | 1.15× | not tested | |
| Phenylpropanoids and polyketides | 1 | 0.9 | 1.13× | not tested | |
| Lipids and lipid-like molecules | 5 | 4.7 | 1.06× | not tested | |
| Organic nitrogen compounds | 1 | 1.4 | 0.74× | not tested |
Unit: a protein (UniProt accession) with a ligand-binding domain in this X-group, counted once per superclass. Expected counts use each superclass's frequency across all ligand-binding X-groups; significance is Fisher's exact test with Benjamini–Hochberg correction. Buffers and crystallization additives are excluded. ECOD v295.2; the method follows the ECOD 2027 update, whose published figures used a slightly different artifact filter.
DrugBank compounds
| DrugBank | PDB ligand | Name | Domains |
|---|---|---|---|
| DB04310 | BB2 | 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide | 70 |
| DB02652 | LHY | L-[(N-Hydroxyamino)Carbonyl]Phenylalanine | 8 |
| DB04368 | BB1 | Bb-3497 | 4 |
| DB08523 | SB7 | [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL | 4 |
| DB00160 | ALA | Alanine | 2 |
| DB02036 | GNR | 2-(3,4-Dihydro-3-Oxo-2h-Benzo[B][1,4]Thiazin-2-Yl)-N-Hydroxyacetamide | 2 |
| DB02276 | MLN | (S)-2-(Phosphonoxy)Caproyl-L-Leucyl-P-Nitroanilide | 2 |
| DB02625 | BRR | (2r)-2-{[Formyl(Hydroxy)Amino]Methyl}Hexanoic Acid | 2 |
| DB02810 | MHA | N-(2-Acetamido)Iminodiacetic Acid | 2 |
| DB03648 | BL5 | (2S,2'S)-2,2'-(1,2-Hydrazinediylbis{methylene[(2S)-1-oxo-2,1-hexanediyl]imino})bis(6-amino-N-phenylhexanamide) | 2 |
| DB04447 | DTT | 1,4-Dithiothreitol | 2 |
| DB00134 | MET | Methionine | 1 |
| DB00145 | GLY | Glycine | 1 |
| DB03345 | BME | Mercaptoethanol | 1 |
| DB04464 | FME | N-Formylmethionine | 1 |
| DB08310 | NVC | N-[(2R)-2-{[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl}hexyl]-N-hydroxyformamide | 1 |
| DB08524 | SB8 | 2-(3-BENZOYLPHENOXY)ETHYL(HYDROXY)FORMAMIDE | 1 |
| DB08525 | SB9 | HYDROXY[3-(6-METHYLPYRIDIN-2-YL)PROPYL]FORMAMIDE | 1 |
| DB08753 | Y12 | 4-{(1E)-3-OXO-3-[(2-PHENYLETHYL)AMINO]PROP-1-EN-1-YL}-1,2-PHENYLENE DIACETATE | 1 |
| DB08754 | Y13 | N-Caffeoyltyramine | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| ZNmetal | ZINC ION | 152 |
| NImetal | NICKEL (II) ION | 91 |
| BB2 | ACTINONIN | 75 |
| COmetal | COBALT (II) ION | 40 |
| CDmetal | CADMIUM ION | 15 |
| FEmetal | FE (III) ION | 14 |
| NAmetal | SODIUM ION | 13 |
| CL | CHLORIDE ION | 10 |
| FE2metal | FE (II) ION | 9 |
| LHY | L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE | 8 |
| K1U | (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid | 7 |
| K3U | S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate | 7 |
| K2U | (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid | 6 |
| H2S | HYDROSULFURIC ACID | 4 |
| MGmetal | MAGNESIUM ION | 4 |
| SB7 | [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL | 4 |
| BB1 | 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEXANOIC ACID (1-DIMETHYLCARBAMOYL-2,2-DIMETHYL-PROPYL)-AMIDE | 3 |
| BB4 | 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | 3 |
| PN3 | tert-butyl {(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl}carbamate | 3 |
| 2BB | (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide | 2 |