Protein profile

PA4414

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase

Genome: NC_002516.2

Gene: murD PA4414 Structure source: Experimental + AlphaFold UniProt Q9HVZ9
Amino acids 448
Annotations 10
Features 20
PDB binders 18
Druggability 0.762

Overview

Basic information about this protein and its source genome.

Accession
PA4414
Gene
murD PA4414
Status
annotated
Amino acids
448
Structure source
Experimental + 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 0.762
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MSLIASDHFRIVVGLGKSGMSLVRYLARRGLPFAVVDTRENPPELATLRAQYPQVEVRCGELDAEFLCSARELYVSPGLSLRTPALVQAAAKGVRISGDIDLFAREAKAPIVAITGSNAKSTVTTLVGEMAVAADKRVAVGGNLGTPALDLLADDIELYVLELSSFQLETCDRLNAEVATVLNVSEDHMDRYDGMADYHLAKHRIFRGARQVVVNRADALTRPLIADTVPCWSFGLNKPDFKAFGLIEEDGQKWLAFQFDKLLPVGELKIRGAHNYSNALAALALGHAVGLPFDAMLGALKAFSGLAHRCQWVRERQGVSYYDDSKATNVGAALAAIEGLGADIDGKLVLLAGGDGKGADFHDLREPVARFCRAVVLLGRDAGLIAQALGNAVPLVRVATLDEAVRQAAELAREGDAVLLSPACASLDMFKNFEERGRLFAKAVEELA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0008764 Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.
  • 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.

20 records
Show feature table
Start End DB Term Name
307 380 Pfam PF02875 Mur ligase family, glutamate ligase domain
307 380 InterPro IPR004101 Mur ligase, C-terminal
10 447 PANTHER PTHR43692 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
10 447 InterPro IPR005762 UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD
100 303 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
100 303 InterPro IPR036565 Mur-like, catalytic domain superfamily
305 447 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
305 447 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
8 442 Hamap MF_00639 UDP-N-acetylmuramoylalanine--D-glutamate ligase [murD].
8 442 InterPro IPR005762 UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD
7 96 Gene3D G3DSA:3.40.50.720 -
12 445 NCBIfam TIGR01087 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase
12 445 InterPro IPR005762 UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD
11 97 SUPERFAMILY SSF51984 MurCD N-terminal domain
311 448 Gene3D G3DSA:3.90.190.20 -
311 448 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
98 305 Gene3D G3DSA:3.40.1190.10 -
98 305 InterPro IPR036565 Mur-like, catalytic domain superfamily
114 285 Pfam PF08245 Mur ligase middle domain
114 285 InterPro IPR013221 Mur ligase, central

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 7SY9
X-ray 1.95 Å A,B
98.4% 8-448
Viewing
PDB 7U35
X-ray 1.95 Å A,B,C
98.4% 8-448
Loaded
PDB 8DP2
X-ray 1.60 Å A
98.2% 9-448
Loaded
AlphaFold PA4414
AlphaFold full sequence Loaded
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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

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
051 P14900 526.5 Da LogP 3.66 TPSA 153.8 1 viol. ✓ Clean c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)NC4C…
ACP Q9HVZ7 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)…
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)…
AZI P14900 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
D17 P14900 499.6 Da LogP 2.84 TPSA 144.8 ✓ Ro5 Alert c1cc(cc(c1)C(=O)N[C@@H](CCC(=O)O)C(=O)O)CNc2ccc…
IK4 P14900 468.5 Da LogP 2.89 TPSA 153.8 ✓ Ro5 ✓ Clean c1cc(ccc1COc2ccc3ccc(cc3c2)S(=O)(=O)NC(CCC(=O)O…
LKM P14900 486.5 Da LogP 3.03 TPSA 153.8 ✓ Ro5 ✓ Clean c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)NC(C…
MLI P14900 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
N04 P14900 484.5 Da LogP 2.64 TPSA 159.1 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)N[C@H](CCC(=O)O)C(=O)O)COc2cccc…
N21 P14900 520.5 Da LogP 2.19 TPSA 176.2 1 viol. ✓ Clean c1cc(ccc1COc2ccc(cc2)\C=C/3\C(=O)NC(=O)S3)S(=O)…
PO3 Q9WY76 79.0 Da LogP -1.64 TPSA 63.2 ✓ Ro5 ✓ Clean [O-][P-](=O)[O-]
T04 P14900 517.6 Da LogP 2.97 TPSA 144.8 1 viol. Alert c1cc(ccc1\C=C/2\C(=O)NC(=S)S2)NCc3ccc(c(c3)C(=O…
T26 P14900 499.6 Da LogP 2.84 TPSA 144.8 ✓ Ro5 Alert c1cc(cc(c1)NCc2ccc(cc2)\C=C/3\C(=O)NC(=S)S3)C(=…
UAG P14900 879.6 Da LogP -5.30 TPSA 427.7 3 viol. ✓ Clean C[C@@H](C(=O)N[C@H](CCC(=O)O)C(=O)O)NC(=O)[C@@H…
UMA P14900 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…
VSV P14900 483.5 Da LogP 2.67 TPSA 161.9 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)N[C@H](CCC(=O)O)C(=O)O)CNc2ccc(…

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.