Protein profile

KP13_01907

UDP-N-acetylmuramoylalanine--D-glutamate ligase

Genome: KpKP13

Gene: murD AHE46348.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GML0
Amino acids 438
Annotations 10
Features 24
PDB binders 18
Druggability 0.372

Overview

Basic information about this protein and its source genome.

Accession
KP13_01907
Gene
murD AHE46348.1
Status
annotated
Amino acids
438
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
89.498
DEG E-value
0.0
Localization
Unknown
ColabFold pLDDT
96.41

Selected Druggability evidence

AlphaFold / UniProt model

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 0.372
Structure A0A0H3GML0
Pocket Pocket 1
P2Rank 0.979
Structure A0A0H3GML0
Pocket Pocket 1
ColabFold model
FPocket 0.482 · Pocket 1
P2Rank 0.986 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

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: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:0008360 Any process that modulates the surface configuration of a cell.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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.
  • 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: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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
7 432 Hamap MF_00639 UDP-N-acetylmuramoylalanine--D-glutamate ligase [murD].
7 432 InterPro IPR005762 UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD
94 299 Gene3D G3DSA:3.40.1190.10 -
94 299 InterPro IPR036565 Mur-like, catalytic domain superfamily
1 437 PANTHER PTHR43692 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
1 437 InterPro IPR005762 UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD
300 434 FunFam G3DSA:3.90.190.20:FF:000003 UDP-N-acetylmuramoylalanine--D-glutamate ligase
9 31 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 93 Gene3D G3DSA:3.40.50.720 -
95 297 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
95 297 InterPro IPR036565 Mur-like, catalytic domain superfamily
1 21 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
301 360 Pfam PF02875 Mur ligase family, glutamate ligase domain
301 360 InterPro IPR004101 Mur ligase, C-terminal
94 299 FunFam G3DSA:3.40.1190.10:FF:000002 UDP-N-acetylmuramoylalanine--D-glutamate ligase
3 94 SUPERFAMILY SSF51984 MurCD N-terminal domain
110 280 Pfam PF08245 Mur ligase middle domain
110 280 InterPro IPR013221 Mur ligase, central
299 437 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
299 437 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
8 435 NCBIfam TIGR01087 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase
8 435 InterPro IPR005762 UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD
300 434 Gene3D G3DSA:3.90.190.20 -
300 434 InterPro IPR036615 Mur ligase, C-terminal domain 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

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GML0
AlphaFold full sequence Viewing
ColabFold KP13_01907
ColabFold 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 0.372
18 0.295

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 30.04 0.933
2 3.44 0.124
3 0.64 0.001

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…
ANP A0A0D5YEC3 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…
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@@]…
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 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…
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.