KpKP13 Protein target profile

UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase

Accession: KP13_01800

Gene: AHE46240.1 lpxD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS43
Length 341
Pocket druggability (P2Rank · AlphaFold DB model) 0.122
Direct ligand evidence 0 68 total records
Functional annotation 1 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.842 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.37 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.122
Structure A0A0H3GS43
Pocket Pocket 1
Druggability (FPocket) 0.707
Structure A0A0H3GS43
Pocket Pocket 1
ColabFold model
P2Rank 0.158 · Pocket 1
FPocket 0.479 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 159 / 4744 genomes with a hit
Prevalence 3.4%

Sequence

Primary amino-acid sequence viewer.

MPSIRLADLAQQLDAELHGDGDIVITGVASMQSAKTGQITFMVNPKYREHLAACQASAVVMTQDDLPFAHSAALVVRNPYLTYARMAQILDTTPQPAQDIAPSAVIDPSAKLGSNVAIGANAVIESGVVLGDNVVIGAGCFVGKNTKIGAGSRLWANVTVYHEIEIGENCLIQSSTVIGADGFGYANDRGNWVKIPQLGRVIIGDRVEIGACTTIDRGALDDTVIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPISEPGVYSSGIPLQPNKAWRKTAALVMNIDEMSKRLKAIERKVNQQD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • GO:0016410 Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0103118 Catalysis of the reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + a (3R)-hydroxyacyl-[ACP] = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + holo-[ACP] + H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
1 99 Gene3D G3DSA:3.40.1390.10 -
33 316 SUPERFAMILY SSF51161 Trimeric LpxA-like enzymes
33 316 InterPro IPR011004 Trimeric LpxA-like superfamily
323 341 Coils Coil Coil
100 309 Gene3D G3DSA:2.160.10.10 Hexapeptide repeat proteins
9 326 Hamap MF_00523 UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase [lpxD].
9 326 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
310 341 Gene3D G3DSA:1.20.5.170 -
145 179 Pfam PF00132 Bacterial transferase hexapeptide (six repeats)
145 179 InterPro IPR001451 Hexapeptide repeat
109 144 Pfam PF00132 Bacterial transferase hexapeptide (six repeats)
109 144 InterPro IPR001451 Hexapeptide repeat
222 255 Pfam PF00132 Bacterial transferase hexapeptide (six repeats)
222 255 InterPro IPR001451 Hexapeptide repeat
130 158 ProSitePatterns PS00101 Hexapeptide-repeat containing-transferases signature.
130 158 InterPro IPR018357 Hexapeptide transferase, conserved site
8 329 NCBIfam TIGR01853 UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
8 329 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
4 338 PANTHER PTHR43378 UDP-3-O-ACYLGLUCOSAMINE N-ACYLTRANSFERASE
4 338 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
100 309 FunFam G3DSA:2.160.10.10:FF:000005 UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
109 314 CDD cd03352 LbH_LpxD
109 314 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
310 341 FunFam G3DSA:1.20.5.170:FF:000032 UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
22 88 Pfam PF04613 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD
22 88 InterPro IPR020573 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region
225 253 ProSitePatterns PS00101 Hexapeptide-repeat containing-transferases signature.
225 253 InterPro IPR018357 Hexapeptide transferase, conserved site

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.122
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Surrounding area
Pocket 2 P2Rank #2
0.01
Likely same site as FPocket 10 2.0 Å 7 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.707
Show in viewer
Surrounding area
Pocket 2 FPocket #7
0.465
Show in viewer
Surrounding area
Pocket 3 FPocket #10
0.239
Likely same site as P2Rank 2 2.0 Å 7 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:239-239 Proton acceptor
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GS43
AlphaFold DB full sequence Viewing
ColabFold KP13_01800
ColabFold full sequence Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 18 records from similar proteins
Structural ligands 18 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1F7 PDB via homolog 584.7 Da · LogP 3.04 · TPSA 182.5 Open detail RCSB PDB
FTT PDB via homolog Detail RCSB PDB
O3V PDB via homolog Detail RCSB PDB
O3Y PDB via homolog Detail RCSB PDB
O4D PDB via homolog Detail RCSB PDB

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
1F7 RCSB PDB P21645 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@H](CC(=O)SCCNC(=O)CCNC(=O)[C@H](C…
FTT RCSB PDB P21645 244.4 Da LogP 3.74 TPSA 57.5 ✓ Ro5 ✓ Clean CCCCCCCCCCC[C@H](CC(=O)O)O
O3V RCSB PDB P21645 389.5 Da LogP 5.01 TPSA 68.0 1 viol. ✓ Clean CC1(Cc2c(c(c3c(n2)nn(c3O)c4ccccc4)c5cccs5)C(=O)…
O3Y RCSB PDB P21645 417.9 Da LogP 5.60 TPSA 68.0 1 viol. ✓ Clean CC1(Cc2c(c(c3c(n2)nn(c3O)c4ccccc4)c5ccccc5Cl)C(…
O4D RCSB PDB P21645 396.5 Da LogP 1.68 TPSA 77.2 ✓ Ro5 ✓ Clean Cc1cc(nc2c1c(nn2CC(=O)NCCCN3CCOCC3)n4cccc4)C
O4G RCSB PDB P21645 364.4 Da LogP 3.56 TPSA 89.8 ✓ Ro5 ✓ Clean c1cc(cc(c1)NC(=O)c2ccco2)NC(=O)c3ccc4c(c3)OCCO4
O4P RCSB PDB P21645 406.5 Da LogP 4.86 TPSA 54.6 ✓ Ro5 ✓ Clean CN([C@@H](c1cccs1)c2c[nH]c3c2cccc3)C(=O)COc4ccc…
O4S RCSB PDB P21645 474.6 Da LogP 3.51 TPSA 73.0 ✓ Ro5 ✓ Clean CCc1ccc(cc1)CNC(=O)CN2c3cc(ccc3N4CCCC[C@@H]4C2=…
O4V RCSB PDB P21645 358.4 Da LogP 2.39 TPSA 100.1 ✓ Ro5 ✓ Clean CCOc1ccccc1n2c(c(nn2)S(=O)(=O)c3ccc(cc3)C)N
PE5 RCSB PDB Q5LH16 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO
PG0 RCSB PDB Q5LH16 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO
PNS RCSB PDB P21645 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
PO3 RCSB PDB B4F258 79.0 Da LogP -1.64 TPSA 63.2 ✓ Ro5 ✓ Clean [O-][P-](=O)[O-]
Q5M RCSB PDB Q9HXY6 228.2 Da LogP 2.89 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)cccc2C(=O)CCC(=O)O
S2N RCSB PDB Q8EZA6 570.7 Da LogP 2.91 TPSA 171.5 1 viol. ✓ Clean CCCCCCCCC[C@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(…
U22 RCSB PDB Q8EZA6 804.7 Da LogP -1.63 TPSA 335.0 3 viol. ✓ Clean CCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@H](O[C@@H…
UD1 RCSB PDB Q5LH16 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@@]…
VFZ RCSB PDB A0A069Q726 405.9 Da LogP 2.31 TPSA 118.1 ✓ Ro5 ✓ Clean c1ccc(c(c1)SCC(=O)N(Cc2nnc(o2)N)CC3=CNC(=O)C=C3…

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.