Protein target profile

PA4416

UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase

Genome: NC_002516.2

Gene: PA4416 murF 3D evidence: Experimental + AlphaFold DB model UniProt Q9HVZ7
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Length 458
Pocket druggability 0.721
Ligand records 68
EC / GO 1 / 11
Target summary

Promising target candidate with multiple supporting evidence streams.

6 signals

Strengths

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.72. This is a computational pocket signal, not binding validation. Structure available Experimental + AlphaFold DB model Direct ligand evidence 1 direct ligand records.

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA4416
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4416 murF
Status
annotated
Amino acids
458
3D evidence
Experimental + AlphaFold DB model
EC
6.3.2.10
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0046872 Binding to a metal ion. GO:0047480 Catalysis of the reaction: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine + ATP + D-alanyl-D-alanine = phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ADP. GO:0008766 Catalysis of the reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine. GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.721
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MLEPLRLSQLTVALDARLIGEDAVFSAVSTDSRAIGPGQLFIALSGPRFDGHDYLAEVAAKGAVAALVEREVADAPLPQLLVRDTRAALGRLGALNRRKFTGPLAAMTGSSGKTTVKEMLASILRTQAGDAESVLATRGNLNNDLGVPLTLLQLAPQHRSAVIELGASRIGEIAYTVELTRPHVAIITNAGTAHVGEFGGPEKIVEAKGEILEGLAADGTAVLNLDDKAFDTWKARASGRPLLTFSLDRPQADFRAADLQRDARGCMGFRLQGVAGEAQVQLNLLGRHNVANALAAAAAAHALGVPLDGIVAGLQALQPVKGRAVAQLTASGLRVIDDSYNANPASMLAAIDILSGFSGRTVLVLGDMGELGSWAEQAHREVGAYAAGKVSALYAVGPLMAHAVQAFGATGRHFADQASLIGALATEQPTTTILIKGSRSAAMDKVVAALCGSSEESH

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046872 Binding to a metal ion.
  • GO:0047480 Catalysis of the reaction: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine + ATP + D-alanyl-D-alanine = phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ADP.
  • GO:0008766 Catalysis of the reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • 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:0009252 The chemical reactions and pathways resulting in the formation 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:0008360 Any process that modulates the surface configuration of a cell.
  • GO:0016881 Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
108 300 Pfam PF08245 Mur ligase middle domain
108 300 InterPro IPR013221 Mur ligase, central
83 317 Gene3D G3DSA:3.40.1190.10 -
83 317 InterPro IPR036565 Mur-like, catalytic domain superfamily
320 391 Pfam PF02875 Mur ligase family, glutamate ligase domain
320 391 InterPro IPR004101 Mur ligase, C-terminal
5 98 SUPERFAMILY SSF63418 MurE/MurF N-terminal domain
5 98 InterPro IPR035911 MurE/MurF, N-terminal
319 451 Gene3D G3DSA:3.90.190.20 -
319 451 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
103 318 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
103 318 InterPro IPR036565 Mur-like, catalytic domain superfamily
26 93 Pfam PF01225 Mur ligase family, catalytic domain
26 93 InterPro IPR000713 Mur ligase, N-terminal catalytic domain
6 456 PANTHER PTHR43024 UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
320 450 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
320 450 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
1 82 Gene3D G3DSA:3.40.1390.10 -
5 451 Hamap MF_02019 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase [murF].
5 451 InterPro IPR005863 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
30 450 NCBIfam TIGR01143 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
30 450 InterPro IPR005863 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

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Structural evidence

3 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 4CVK
X-ray 1.92 Å A
100.0% 1-458
PDBe RCSB PDBj File
Viewing
PDB 4CVM
X-ray 2.06 Å A
100.0% 1-458
PDBe RCSB PDBj File
Loaded
PDB 4CVL
X-ray 2.98 Å A
100.0% 1-458
PDBe RCSB PDBj File
Loaded
AlphaFold DB PA4416
AlphaFold DB — — full sequence — Loaded
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #7
0.721
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Site 2 FPocket #1
0.466
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Site 3 FPocket #2
0.284
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Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.207
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Site 2 P2Rank #2
0.112
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Site 3 P2Rank #3
0.06
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Site 4 P2Rank #4
0.035
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Site 5 P2Rank #5
0.028
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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.

68 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 1 67 via homologs
Structural ligands 9 1 loaded crystals
Bioactive compounds 9 50 ZINC proposed compounds
Drug-like & clean 30 0 PAINS alerts
Best available ligand signal
ACP PDB co-crystal 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
Detail RCSB PDB ACP PDB co-crystal
Detail RCSB PDB 1LG PDB via homolog
Detail RCSB PDB 2GN PDB via homolog
Detail RCSB PDB 2LG PDB via homolog

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
ACP RCSB PDB
4CVL 2.98 Å Open crystal
505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.