Protein profile

KP13_31828

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

Genome: KpKP13

Gene: murE AHE46351.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJ91
Amino acids 495
Annotations 11
Features 28
PDB binders 18
Druggability 0.742

Overview

Basic information about this protein and its source genome.

Accession
KP13_31828
Gene
murE AHE46351.1
Status
annotated
Amino acids
495
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 (%)
92.323
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.58

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 0.742
Structure A0A0H3GJ91
Pocket Pocket 2
P2Rank 0.979
Structure A0A0H3GJ91
Pocket Pocket 1
ColabFold model
FPocket 0.426 · Pocket 14
P2Rank 0.986 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • 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:0000287 Binding to a magnesium (Mg) ion.
  • GO:0008765 Catalysis of the reaction: meso-2,6-diaminopimelate + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate.
  • 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.

28 records
Show feature table
Start End DB Term Name
344 495 FunFam G3DSA:3.90.190.20:FF:000006 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
342 494 Gene3D G3DSA:3.90.190.20 -
342 494 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
2 104 Gene3D G3DSA:3.40.1390.10 -
339 491 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
339 491 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
339 425 Pfam PF02875 Mur ligase family, glutamate ligase domain
339 425 InterPro IPR004101 Mur ligase, C-terminal
25 102 Pfam PF01225 Mur ligase family, catalytic domain
25 102 InterPro IPR000713 Mur ligase, N-terminal catalytic domain
22 491 NCBIfam TIGR01085 UDP-N-acetylmuramyl-tripeptide synthetase
22 491 InterPro IPR005761 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase
4 491 Hamap MF_00208 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase [murE].
4 491 InterPro IPR005761 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase
2 104 FunFam G3DSA:3.40.1390.10:FF:000002 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
328 495 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
306 327 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
114 318 Pfam PF08245 Mur ligase middle domain
114 318 InterPro IPR013221 Mur ligase, central
105 341 FunFam G3DSA:3.40.1190.10:FF:000006 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
105 338 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
105 338 InterPro IPR036565 Mur-like, catalytic domain superfamily
105 341 Gene3D G3DSA:3.40.1190.10 -
105 341 InterPro IPR036565 Mur-like, catalytic domain superfamily
5 103 SUPERFAMILY SSF63418 MurE/MurF N-terminal domain
5 103 InterPro IPR035911 MurE/MurF, N-terminal
1 305 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 494 PANTHER PTHR23135 MUR LIGASE FAMILY MEMBER

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

Loading 3D structure...

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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_A0A0H3GJ91
AlphaFold full sequence Viewing
ColabFold KP13_31828
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
2 0.742

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 31.78 0.94
2 8.29 0.442

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.

77 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…
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 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)…
API P22188 190.2 Da LogP -1.02 TPSA 126.6 ✓ Ro5 ✓ Clean C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
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…
JHP P22188 227.7 Da LogP 1.75 TPSA 46.9 ✓ Ro5 ✓ Clean Cn1cc(c(n1)C(=O)NC2CCCC2)Cl
LVV P22188 239.3 Da LogP 1.23 TPSA 37.4 ✓ Ro5 ✓ Clean Cc1ccc(cc1)CN2CCS(=O)(=O)CC2
O3D P22188 215.3 Da LogP 0.51 TPSA 50.5 ✓ Ro5 ✓ Clean c1cc(oc1)CN2CCS(=O)(=O)CC2
SYQ P22188 204.3 Da LogP 1.92 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1cccc(n1)C(=O)N[C@@H](C)C2CC2
SYZ P22188 278.3 Da LogP 1.42 TPSA 66.5 ✓ Ro5 ✓ Clean Cc1cccc(c1)C(=O)NCCN2C(=O)CSC2=O
SZK P22188 241.3 Da LogP 3.26 TPSA 43.0 ✓ Ro5 ✓ Clean CCn1c2ccccc2nc1NCc3ccco3
SZN P22188 260.3 Da LogP 0.87 TPSA 66.5 ✓ Ro5 ✓ Clean Cc1cccc(c1)C(=O)NCCN2C(=O)CCC2=O
T3Z P22188 204.3 Da LogP 1.92 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1cccc(n1)C(=O)N[C@H](C)C2CC2
UAG P22188 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…
UML Q2FZP6 1007.8 Da LogP -5.68 TPSA 482.8 3 viol. ✓ Clean C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCCCN)C(=O)O…
WZD P22188 213.2 Da LogP 2.77 TPSA 53.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]c(n2)NCc3ccco3

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.