Protein profile

KP13_01909

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

Genome: KpKP13

Gene: AHE46350.1 murF Structure source: AlphaFold + ColabFold UniProt A0A0H3GRQ0
Amino acids 452
Annotations 5
Features 28
PDB binders 18
Druggability 0.458

Overview

Basic information about this protein and its source genome.

Accession
KP13_01909
Gene
AHE46350.1 murF
Status
annotated
Amino acids
452
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 (%)
84.071
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.99

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 0.458
Structure A0A0H3GRQ0
Pocket Pocket 29
P2Rank 0.975
Structure A0A0H3GRQ0
Pocket Pocket 1
ColabFold model
FPocket 0.126 · Pocket 26
P2Rank 0.976 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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: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: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: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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
29 446 NCBIfam TIGR01143 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
29 446 InterPro IPR005863 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
1 15 Phobius SIGNAL_PEPTIDE Signal peptide region
81 310 Gene3D G3DSA:3.40.1190.10 -
81 310 InterPro IPR036565 Mur-like, catalytic domain superfamily
1 97 SUPERFAMILY SSF63418 MurE/MurF N-terminal domain
1 97 InterPro IPR035911 MurE/MurF, N-terminal
1 80 Gene3D G3DSA:3.40.1390.10 -
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
101 310 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
101 310 InterPro IPR036565 Mur-like, catalytic domain superfamily
1 449 PANTHER PTHR43024 UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
12 15 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
4 11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
106 292 Pfam PF08245 Mur ligase middle domain
106 292 InterPro IPR013221 Mur ligase, central
313 446 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
313 446 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
16 452 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
313 391 Pfam PF02875 Mur ligase family, glutamate ligase domain
313 391 InterPro IPR004101 Mur ligase, C-terminal
4 447 Hamap MF_02019 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase [murF].
4 447 InterPro IPR005863 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
312 452 Gene3D G3DSA:3.90.190.20 -
312 452 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
81 310 FunFam G3DSA:3.40.1190.10:FF:000007 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
24 95 Pfam PF01225 Mur ligase family, catalytic domain
24 95 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.

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_A0A0H3GRQ0
AlphaFold full sequence Viewing
ColabFold KP13_01909
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
29 0.458
1 0.355
20 0.213

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 30.28 0.934
2 1.82 0.035
3 1.68 0.028

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.