Protein profile

PA5485

protein AmpDh2

Genome: NC_002516.2

Gene: ampDh2 PA5485 Structure source: Experimental + AlphaFold UniProt Q9HT86
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Amino acids 259
Annotations 8
Features 26
PDB binders 2
Druggability 0.572

Overview

Basic information about this protein and its source genome.

Accession
PA5485
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
ampDh2 PA5485
Status
annotated
Amino acids
259
Structure source
Experimental + AlphaFold
EC
3.5.1.28
GO
GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain. GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. GO:0046872 Binding to a metal ion. GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides. GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. GO:0009253 The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.572
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
  • GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
  • GO:0046872 Binding to a metal ion.
  • GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0009253 The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
194 255 SUPERFAMILY SSF47090 PGBD-like
194 255 InterPro IPR036365 PGBD-like superfamily
4 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
180 259 Gene3D G3DSA:1.10.101.10 -
180 259 InterPro IPR036366 PGBD superfamily
34 179 Gene3D G3DSA:3.40.80.10 -
34 179 InterPro IPR036505 N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
199 253 Pfam PF01471 Putative peptidoglycan binding domain
199 253 InterPro IPR002477 Peptidoglycan binding-like
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
1 20 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
34 179 FunFam G3DSA:3.40.80.10:FF:000003 N-acetylmuramoyl-L-alanine amidase
34 166 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase
34 166 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
35 167 CDD cd06583 PGRP
35 167 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
24 254 PANTHER PTHR30417 N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
24 165 SMART SM00644 ami_2
24 165 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
20 259 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22 177 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like
22 177 InterPro IPR036505 N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
1 17 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
15 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

3D Structure

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

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Structural evidence

3 + 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 4BOL
X-ray 1.70 Å A,B
100.0% 1-259
PDBe RCSB PDBj File
Viewing
PDB 4BPA
X-ray 2.70 Å A,B
100.0% 1-259
PDBe RCSB PDBj File
Loaded
PDB 4BJ4
X-ray 1.72 Å A,B
93.4% 18-259
PDBe RCSB PDBj File
Loaded
AlphaFold PA5485
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
2 0.572
1 0.281
5 0.25

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 5.02 0.228
2 2.59 0.074
3 2.49 0.069

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.

48 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
FLC
4BJ4 1.72 Å Open crystal
189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
J0J
4BOL 1.70 Å Open crystal
461.5 Da LogP -2.66 TPSA 251.2 1 viol. ✓ Clean C[C@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=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.