Protein profile

PA0019

peptide deformylase

Genome: NC_002516.2

Gene: def PA0019 Structure source: Experimental + AlphaFold UniProt Q9I7A8
Amino acids 168
Annotations 4
Features 25
PDB binders 12
Druggability 0.804

Overview

Basic information about this protein and its source genome.

Accession
PA0019
Gene
def PA0019
Status
annotated
Amino acids
168
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.727
Human E-value
5.87e-20
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.804
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0046872 Binding to a metal ion.
  • GO:0042586 Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
  • GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
4 161 NCBIfam TIGR00079 peptide deformylase
4 161 InterPro IPR023635 Peptide deformylase
1 168 FunFam G3DSA:3.90.45.10:FF:000001 Peptide deformylase
1 168 Gene3D G3DSA:3.90.45.10 Peptide deformylase
1 168 InterPro IPR036821 Peptide deformylase superfamily
90 101 PRINTS PR01576 Peptide deformylase signature
90 101 InterPro IPR023635 Peptide deformylase
102 120 PRINTS PR01576 Peptide deformylase signature
102 120 InterPro IPR023635 Peptide deformylase
121 150 PRINTS PR01576 Peptide deformylase signature
121 150 InterPro IPR023635 Peptide deformylase
33 62 PRINTS PR01576 Peptide deformylase signature
33 62 InterPro IPR023635 Peptide deformylase
2 163 Hamap MF_00163 Peptide deformylase [def].
2 163 InterPro IPR023635 Peptide deformylase
1 168 PIRSF PIRSF004749 Pep_def
1 168 InterPro IPR023635 Peptide deformylase
4 153 Pfam PF01327 Polypeptide deformylase
4 153 InterPro IPR023635 Peptide deformylase
6 144 CDD cd00487 Pep_deformylase
6 144 InterPro IPR023635 Peptide deformylase
3 163 PANTHER PTHR10458 PEPTIDE DEFORMYLASE
3 163 InterPro IPR023635 Peptide deformylase
2 165 SUPERFAMILY SSF56420 Peptide deformylase
2 165 InterPro IPR036821 Peptide deformylase superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

5 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 1N5N
X-ray 1.80 Å A,B
100.0% 1-168
Viewing
PDB 1IX1
X-ray 1.85 Å A,B
100.0% 1-168
Loaded
PDB 8S1X
X-ray 1.88 Å A
100.0% 1-168
Loaded
PDB 1S17
X-ray 1.95 Å A,B
100.0% 1-168
Loaded
PDB 1LRY
X-ray 2.60 Å A
99.4% 2-168
Loaded
AlphaFold PA0019
AlphaFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.804

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 16.48 0.779

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

107 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
BB2 385.5 Da LogP 1.20 TPSA 119.0 ✓ Ro5 ✓ Clean CCCCC[C@H](CC(=O)NO)C(=O)N[C@@H](C(C)C)C(=O)N1C…
GNR 238.3 Da LogP 0.99 TPSA 78.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)NC(=O)[C@H](S2)CC(=O)NO
MHA 190.2 Da LogP -2.06 TPSA 120.9 ✓ Ro5 ✓ Clean C(C(=O)N)N(CC(=O)O)CC(=O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.