Protein profile

KP13_01899

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

Genome: KpKP13

Gene: lpxC AHE46340.1 Structure source: AlphaFold + ColabFold UniProt A6T4N9
Amino acids 305
Annotations 2
Features 18
PDB binders 41
Druggability 0.902

Overview

Basic information about this protein and its source genome.

Accession
KP13_01899
Gene
lpxC AHE46340.1
Status
annotated
Amino acids
305
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 (%)
96.066
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.55

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 0.902
Structure A6T4N9
Pocket Pocket 2
P2Rank 0.935
Structure A6T4N9
Pocket Pocket 1
ColabFold model
FPocket 0.455 · Pocket 9
P2Rank 0.941 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 273 / 4744 genomes with a hit
Normalized 0.058

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0008759 OBSOLETE. Catalysis of the removal of an acetyl group from the 2-N position of glucosamine in the lipid A precursor UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 128 Gene3D G3DSA:3.30.230.20 lpxc deacetylase, domain 1
1 128 InterPro IPR015870 UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal
4 276 Pfam PF03331 UDP-3-O-acyl N-acetylglycosamine deacetylase
4 276 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
1 128 FunFam G3DSA:3.30.230.20:FF:000001 UDP-3-O-acyl-N-acetylglucosamine deacetylase
2 280 Hamap MF_00388 UDP-3-O-acyl-N-acetylglucosamine deacetylase [lpxC].
2 280 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
129 305 Gene3D G3DSA:3.30.1700.10 lpxc deacetylase, domain 2
129 305 InterPro IPR011334 UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal
2 301 NCBIfam TIGR00325 UDP-3-O-acyl-N-acetylglucosamine deacetylase
2 301 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
3 124 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
3 124 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
3 285 PANTHER PTHR33694 UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE 1, MITOCHONDRIAL-RELATED
3 285 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
129 305 FunFam G3DSA:3.30.1700.10:FF:000001 UDP-3-O-acyl-N-acetylglucosamine deacetylase
134 278 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
134 278 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold

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_A6T4N9
AlphaFold full sequence Viewing
ColabFold KP13_01899
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 0.902

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 22.66 0.882
2 2.63 0.076
3 1.75 0.032
4 1.31 0.014

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.

191 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
03I P47205 490.6 Da LogP 2.70 TPSA 105.2 ✓ Ro5 ✓ Clean C[C@@](CCc1ccc(cc1)c2ccc(cc2)OCCCN3CCOCC3)(C(=O…
1JS P47205 423.5 Da LogP 0.97 TPSA 127.8 ✓ Ro5 ✓ Clean c1ccc(cc1)C#Cc2ccc(cc2)C(=O)NC(CCC(=O)NCCCO)C(=…
1WL P47205 413.4 Da LogP 1.24 TPSA 133.1 ✓ Ro5 ✓ Clean c1cc(ccc1C#CC#Cc2ccc(cc2)N)C(=O)NC(Cc3cnc[nH]3)…
1WM P47205 455.5 Da LogP 1.71 TPSA 144.9 1 viol. ✓ Clean c1cc(ccc1C#CC#Cc2ccc(cc2)N)C(=O)NC(C(c3ccc(cc3)…
1WN P47205 469.5 Da LogP 1.89 TPSA 144.9 1 viol. ✓ Clean CC(c1ccc(cc1)O)(C(C(=O)NO)NC(=O)c2ccc(cc2)C#CC#…
2CW P0A725 389.4 Da LogP 1.83 TPSA 121.8 ✓ Ro5 ✓ Clean CC(C(C)(C(=O)N=O)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc…
2SZ P47205 543.6 Da LogP 3.75 TPSA 99.4 1 viol. ✓ Clean CN1CCN(CC1)Cc2ccc(cn2)C#Cc3ccc(cc3)c4cc(cnc4n5c…
3P3 P47205 362.4 Da LogP 1.07 TPSA 98.7 ✓ Ro5 ✓ Clean CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccccc2)O
5EM P47205 390.4 Da LogP 1.01 TPSA 130.5 ✓ Ro5 ✓ Clean CC(C)(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc2…
5EN P47205 427.4 Da LogP 1.29 TPSA 124.7 ✓ Ro5 ✓ Clean CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc2)N)…
7TD P47205 319.4 Da LogP 0.43 TPSA 113.7 ✓ Ro5 ✓ Clean CC#CCOc1ccc(cc1)C(=O)NC(C(=O)NO)C(C)(C)N
8GJ P47205 412.4 Da LogP 1.36 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@@](CCN1C=CC(=CC1=O)c2ccc(cc2F)OC)(C(=O)NO)S…
8Q8 P47205 473.6 Da LogP 2.01 TPSA 125.4 ✓ Ro5 ✓ Clean CC(C)(C(C(=O)NO)NC1CCc2c1ccc(c2)C#Cc3ccc(cc3)Cn…
A5F P47205 369.4 Da LogP 0.01 TPSA 124.7 ✓ Ro5 ✓ Clean CC(C)(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#CC2CC2CO)N
C90 A1JJJ9 437.5 Da LogP 0.90 TPSA 111.1 ✓ Ro5 ✓ Clean CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#Cc2ccc(cc2)CN3CC…
EU1 Q02H34 538.0 Da LogP 2.64 TPSA 135.1 1 viol. ✓ Clean C[C@@](CCN1CC=C(CC1=O)c2ccc(cc2)OCc3cc(c(nc3)OC…
F64 Q02H34 538.0 Da LogP 2.64 TPSA 135.1 1 viol. ✓ Clean C[C@](CCN1CC=C(CC1=O)c2ccc(cc2)OCc3cc(c(nc3)OC)…
FXU P47205 340.3 Da LogP 1.29 TPSA 98.5 ✓ Ro5 ✓ Clean CS(=O)(=O)CC[C@H](C(=O)Nc1cccc(c1)OC(F)(F)F)N
FXX P47205 292.2 Da LogP 1.33 TPSA 101.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)OC(F)(F)F)NC(=O)[C@@H](CC(=O)O)N
FY6 P47205 264.8 Da LogP 3.22 TPSA 38.0 ✓ Ro5 ✓ Clean C[C@@H](c1nccn1CCCc2ccc(cc2)Cl)O
FY9 P47205 484.6 Da LogP 1.09 TPSA 120.9 ✓ Ro5 ✓ Clean CS(=O)(=O)CC(C(C(=O)N1CCC(CC1)Cc2ccc(cc2)C#Cc3c…
FYF P47205 269.3 Da LogP 2.64 TPSA 64.1 ✓ Ro5 ✓ Clean C[C@@H](c1nccn1Cc2cc(on2)c3ccccc3)O
FYL P47205 412.4 Da LogP 0.43 TPSA 139.8 ✓ Ro5 ✓ Clean CC(c1nccn1Cc2cc(on2)C#Cc3ccc(cc3)OCC(CO)(CO)N)O
FYR P47205 214.2 Da LogP 2.76 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(c(c2)O)C(=O)O
FZ0 P47205 234.2 Da LogP 1.48 TPSA 64.3 ✓ Ro5 ✓ Clean c1cc(cc(c1)OC(F)(F)F)NC(=O)CN
FZ3 P47205 220.7 Da LogP 3.17 TPSA 17.8 ✓ Ro5 ✓ Clean c1cc(ccc1CCCn2ccnc2)Cl
FZ6 P47205 264.2 Da LogP 0.84 TPSA 84.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)OC(F)(F)F)NC(=O)[C@@H](CO)N
HAY B7UZI4 470.5 Da LogP 2.79 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@@](CCN1C=CC(=CC1=O)c2ccc(cc2)OCc3ccccc3)(C(…
HUM P47205 488.5 Da LogP 2.93 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@](CCN1C=CC(=CC1=O)c2ccc(cc2F)OCc3ccccc3)(C(…
J1M B7UZI4 470.5 Da LogP 2.79 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@](CCN1C=CC(=CC1=O)c2ccc(cc2)OCc3ccccc3)(C(=…
JBA P47205 406.5 Da LogP 1.47 TPSA 113.0 ✓ Ro5 ✓ Clean CC(CC1CN(C(=O)O1)c2ccc(cc2)C#CC3CC3)(C(=O)NO)S(…
JCG P47205 488.5 Da LogP 2.93 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@@](CCN1C=CC(=CC1=O)c2ccc(cc2F)OCc3ccccc3)(C…
JWM P47205 406.5 Da LogP -0.15 TPSA 132.8 ✓ Ro5 ✓ Clean CC(C)(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#CCCO)S(=O)…
JWP P47205 462.5 Da LogP -0.13 TPSA 142.0 ✓ Ro5 ✓ Clean CC(C)(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#CCCO)S(=O)…
JWV P47205 420.4 Da LogP -1.16 TPSA 142.0 ✓ Ro5 ✓ Clean COC1(CS(=O)(=O)C1)C(C(=O)NO)NC(=O)c2ccc(cc2)C#C…
L52 P47205 347.4 Da LogP 0.65 TPSA 104.5 ✓ Ro5 ✓ Clean c1ccc(cc1)C#CC#Cc2ccc(cc2)C(=O)NC(CN)C(=O)NO
L58 P47205 393.2 Da LogP 2.10 TPSA 98.7 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)NO)NC(=O)c1ccc(cc1)c2ccc(cc2…
L59 P47205 338.4 Da LogP 1.07 TPSA 98.7 ✓ Ro5 ✓ Clean CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#Cc2ccccc2)O
L63 P47205 314.3 Da LogP 1.34 TPSA 98.7 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)NO)NC(=O)c1ccc(cc1)c2ccccc2)O
MPB P47205 152.1 Da LogP 1.18 TPSA 46.5 ✓ Ro5 ✓ Clean COC(=O)c1ccc(cc1)O
UKW P0A725 260.2 Da LogP 0.44 TPSA 95.8 ✓ Ro5 ✓ Clean CC(C(C(=O)N=O)NC(=O)c1ccc(cc1)C#C)O

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.