Protein profile

PA4020

UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase

Genome: NC_002516.2

Gene: mpl PA4020 Structure source: AlphaFold UniProt Q9HX07
Amino acids 451
Annotations 12
Features 28
PDB binders 10
Druggability 0.821

Overview

Basic information about this protein and its source genome.

Accession
PA4020
Gene
mpl PA4020
Status
annotated
Amino acids
451
Structure source
AlphaFold

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 0.821
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

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:0106418 Catalysis of the reaction: ATP + UDP-N-acetyl-alpha-D-muramate + L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate.
  • 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:0071236 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
  • 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: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.
  • 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.

28 records
Show feature table
Start End DB Term Name
1 450 Hamap MF_02020 UDP-N-acetylmuramate--L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase [mpl].
1 450 InterPro IPR005757 Murein peptide ligase
1 90 Gene3D G3DSA:3.40.50.720 -
108 291 Pfam PF08245 Mur ligase middle domain
108 291 InterPro IPR013221 Mur ligase, central
2 449 NCBIfam TIGR01081 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase
2 449 InterPro IPR005757 Murein peptide ligase
314 451 Gene3D G3DSA:3.90.190.20 -
314 451 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
311 360 Pfam PF02875 Mur ligase family, glutamate ligase domain
311 360 InterPro IPR004101 Mur ligase, C-terminal
5 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
21 451 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 20 SignalP_EUK SignalP-noTM SignalP-noTM
2 450 PANTHER PTHR43445 UDP-N-ACETYLMURAMATE--L-ALANINE LIGASE-RELATED
91 313 Gene3D G3DSA:3.40.1190.10 -
91 313 InterPro IPR036565 Mur-like, catalytic domain superfamily
94 308 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
94 308 InterPro IPR036565 Mur-like, catalytic domain superfamily
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 90 FunFam G3DSA:3.40.50.720:FF:000161 UDP-N-acetylmuramate--L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase
311 448 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
311 448 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
1 90 SUPERFAMILY SSF51984 MurCD N-terminal domain
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
17 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
2 100 Pfam PF01225 Mur ligase family, catalytic domain
2 100 InterPro IPR000713 Mur ligase, N-terminal catalytic domain

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

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4020
AlphaFold full sequence Viewing
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 0.278

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.

69 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1LG Q8DNV6 500.4 Da LogP 4.08 TPSA 99.5 1 viol. ✓ Clean c1c(c(cc(c1S(=O)(=O)N2CCOCC2)Cl)Cl)C(=O)Nc3c(c4…
2GN Q8DNV6 659.6 Da LogP 3.94 TPSA 157.2 1 viol. ✓ Clean c1cc(ccc1CN2CCc3c(sc(c3C#N)NC(=O)c4cc(c(cc4Cl)C…
2LG Q8DNV6 438.0 Da LogP 4.04 TPSA 90.3 ✓ Ro5 ✓ Clean CCN(CC)S(=O)(=O)c1ccc(c(c1)C(=O)Nc2c(c3c(s2)CCC…
ANP B7GV74 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
EPU P45066 677.4 Da LogP -4.03 TPSA 332.2 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
IGM Q8DNV6 607.5 Da LogP 4.46 TPSA 123.0 1 viol. ✓ Clean c1cc(ccc1CN2CCc3c(sc(c3C#N)NC(=O)c4cc(c(cc4Cl)C…
UD1 P65473 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
UMA P45066 750.5 Da LogP -4.65 TPSA 361.3 3 viol. ✓ Clean C[C@@H](C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@…
UXP Q9HW02 354.4 Da LogP 2.05 TPSA 118.6 ✓ Ro5 ✓ Clean c1c([nH]nc1Nc2c3c[nH]nc3nc(n2)N4CCCC[C@@H]4CO)C…
UYD Q9HW02 406.5 Da LogP 3.27 TPSA 116.6 ✓ Ro5 ✓ Clean CC(C)(C)c1cc(nn1C)Nc2c3cn[nH]c3nc(n2)N[C@@H](CO…

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.