Protein profile

PA4406

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

Genome: NC_002516.2

Gene: envA lpxC PA4406 Structure source: Experimental + AlphaFold UniProt P47205
Amino acids 303
Annotations 7
Features 18
PDB binders 54
Druggability 0.723

Overview

Basic information about this protein and its source genome.

Accession
PA4406
Gene
envA lpxC PA4406
Status
annotated
Amino acids
303
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.723
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0046872 Binding to a metal ion.
  • GO:0103117 Catalysis of the reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
128 303 Gene3D G3DSA:3.30.1700.10 lpxc deacetylase, domain 2
128 303 InterPro IPR011334 UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal
3 284 PANTHER PTHR33694 UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE 1, MITOCHONDRIAL-RELATED
3 284 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
128 303 FunFam G3DSA:3.30.1700.10:FF:000001 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
1 127 Gene3D G3DSA:3.30.230.20 lpxc deacetylase, domain 1
1 127 InterPro IPR015870 UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal
134 277 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
134 277 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
4 275 Pfam PF03331 UDP-3-O-acyl N-acetylglycosamine deacetylase
4 275 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
1 127 FunFam G3DSA:3.30.230.20:FF:000001 UDP-3-O-acyl-N-acetylglucosamine deacetylase
2 298 NCBIfam TIGR00325 UDP-3-O-acyl-N-acetylglucosamine deacetylase
2 298 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
2 279 Hamap MF_00388 UDP-3-O-acyl-N-acetylglucosamine deacetylase [lpxC].
2 279 InterPro IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase

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

64 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 6CAX
X-ray 1.25 Å A
100.0% 1-303
Viewing
PDB 3UHM
X-ray 1.26 Å A
98.7% 1-299
Loaded
PDB 3P3E
X-ray 1.28 Å A
98.7% 1-299
Loaded
PDB 6DUI
X-ray 1.55 Å A
100.0% 1-303
Loaded
PDB 4LCG
X-ray 1.57 Å A
98.7% 1-299
Loaded
PDB 5DRR
X-ray 1.59 Å A
98.7% 1-299
Loaded
PDB 4LCF
X-ray 1.60 Å A
98.7% 1-299
Loaded
PDB 4LCH
X-ray 1.60 Å A
98.7% 1-299
Loaded
PDB 7CIB
X-ray 1.61 Å A
98.7% 1-299
Loaded
PDB 5DRQ
X-ray 1.63 Å A
98.7% 1-299
Loaded
PDB 6E54
X-ray 1.65 Å A
100.0% 1-303
Loaded
PDB 5UPG
X-ray 1.70 Å A
100.0% 1-303
Loaded
PDB 4FW7
X-ray 1.70 Å A,B,C,D
98.7% 1-299
Loaded
PDB 5U39
X-ray 1.75 Å A
96.4% 2-293
Loaded
PDB 7CIC
X-ray 1.78 Å A,B
98.7% 1-299
Loaded
PDB 5VWM
X-ray 1.80 Å A
100.0% 1-303
Loaded
PDB 6MAE
X-ray 1.80 Å A
98.7% 1-299
Loaded
PDB 7PJ2
X-ray 1.80 Å A
98.7% 1-299
Loaded
PDB 4FW6
X-ray 1.83 Å A,B,C,D
98.7% 1-299
Loaded
PDB 6MO4
X-ray 1.84 Å A
98.3% 2-299
Loaded
PDB 6MO5
X-ray 1.85 Å A
98.3% 2-299
Loaded
PDB 6MOD
X-ray 1.85 Å A
98.3% 2-299
Loaded
PDB 5N8C
X-ray 1.90 Å A,B
100.0% 1-303
Loaded
PDB 7K99
X-ray 1.90 Å A,C
100.0% 1-303
Loaded
PDB 2VES
X-ray 1.90 Å A,B,C
98.7% 1-299
Loaded
PDB 7CI9
X-ray 1.90 Å A
98.7% 1-299
Loaded
PDB 7DEM
X-ray 1.90 Å A
98.7% 1-299
Loaded
PDB 7PHN
X-ray 1.90 Å A
98.7% 1-299
Loaded
PDB 7CIA
X-ray 1.92 Å A
98.7% 1-299
Loaded
PDB 7PZV
X-ray 1.92 Å A
98.7% 1-299
Loaded
PDB 4FW5
X-ray 1.99 Å A,B,C,D
98.7% 1-299
Loaded
PDB 6C9C
X-ray 2.00 Å A
100.0% 1-303
Loaded
PDB 7K9A
X-ray 2.00 Å A,C
100.0% 1-303
Loaded
PDB 3U1Y
X-ray 2.00 Å A,B
98.7% 1-299
Loaded
PDB 5U3B
X-ray 2.00 Å A,B
98.7% 1-299
Loaded
PDB 7CI4
X-ray 2.00 Å A,B
98.7% 1-299
Loaded
PDB 7PZW
X-ray 2.00 Å A
98.7% 1-299
Loaded
PDB 4J3D
X-ray 2.00 Å A,B
98.0% 1-297
Loaded
PDB 7Q01
X-ray 2.01 Å A
98.7% 1-299
Loaded
PDB 8E4A
X-ray 2.03 Å A
98.7% 1-299
Loaded
PDB 7PJG
X-ray 2.04 Å A
98.7% 1-299
Loaded
PDB 4OKG
X-ray 2.06 Å A,B
98.7% 1-299
Loaded
PDB 7DEN
X-ray 2.07 Å A
98.7% 1-299
Loaded
PDB 7CI7
X-ray 2.10 Å A
98.7% 1-299
Loaded
PDB 7PKM
X-ray 2.10 Å A
98.7% 1-299
Loaded
PDB 7CIE
X-ray 2.15 Å A,B
98.7% 1-299
Loaded
PDB 7DEL
X-ray 2.15 Å A
98.7% 1-299
Loaded
PDB 7PZU
X-ray 2.15 Å A
98.7% 1-299
Loaded
PDB 4FW4
X-ray 2.19 Å A,B,C,D
98.7% 1-299
Loaded
PDB 6MOO
X-ray 2.20 Å A
98.3% 2-299
Loaded
PDB 7PK8
X-ray 2.30 Å A
98.7% 1-299
Loaded
PDB 4FW3
X-ray 2.35 Å A,B,C,D
98.7% 1-299
Loaded
PDB 7PZX
X-ray 2.39 Å A
98.7% 1-299
Loaded
PDB 7PZS
X-ray 2.45 Å A
98.7% 1-299
Loaded
PDB 7CID
X-ray 2.49 Å A
98.7% 1-299
Loaded
PDB 7CI5
X-ray 2.50 Å A,B,C,D
98.7% 1-299
Loaded
PDB 7PKK
X-ray 2.55 Å A
98.7% 1-299
Loaded
PDB 7CI6
X-ray 2.70 Å A,B
98.7% 1-299
Loaded
PDB 7CI8
X-ray 3.00 Å A,B
98.7% 1-299
Loaded
PDB 6I46
X-ray 1.75 Å AAA
98.7% 1-299
PDB 6I47
X-ray 1.90 Å AAA
98.7% 1-299
PDB 6I49
X-ray 1.94 Å AAA,BBB
98.7% 1-299
PDB 6I48
X-ray 2.20 Å AAA
98.7% 1-299
PDB 6I4A
X-ray 2.25 Å AAA
98.7% 1-299
AlphaFold PA4406
AlphaFold 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 0.723
2 0.506

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 40.14 0.963
2 13.62 0.693
3 3.42 0.123
4 2.07 0.046
5 0.94 0.004

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.

204 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
1JS 423.5 Da LogP 0.97 TPSA 127.8 ✓ Ro5 ✓ Clean c1ccc(cc1)C#Cc2ccc(cc2)C(=O)NC(CCC(=O)NCCCO)C(=…
1WL 413.4 Da LogP 1.24 TPSA 133.1 ✓ Ro5 ✓ Clean c1cc(ccc1C#CC#Cc2ccc(cc2)N)C(=O)NC(Cc3cnc[nH]3)…
1WM 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 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#…
2SZ 543.6 Da LogP 3.75 TPSA 99.4 1 viol. ✓ Clean CN1CCN(CC1)Cc2ccc(cn2)C#Cc3ccc(cc3)c4cc(cnc4n5c…
3P3 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 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 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 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 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 473.6 Da LogP 2.01 TPSA 125.4 ✓ Ro5 ✓ Clean CC(C)(C(C(=O)NO)NC1CCc2c1ccc(c2)C#Cc3ccc(cc3)Cn…
A5F 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 437.5 Da LogP 0.90 TPSA 111.1 ✓ Ro5 ✓ Clean CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#Cc2ccc(cc2)CN3CC…
FXU 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 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 264.8 Da LogP 3.22 TPSA 38.0 ✓ Ro5 ✓ Clean C[C@@H](c1nccn1CCCc2ccc(cc2)Cl)O
FY9 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 269.3 Da LogP 2.64 TPSA 64.1 ✓ Ro5 ✓ Clean C[C@@H](c1nccn1Cc2cc(on2)c3ccccc3)O
FYL 412.4 Da LogP 0.43 TPSA 139.8 ✓ Ro5 ✓ Clean CC(c1nccn1Cc2cc(on2)C#Cc3ccc(cc3)OCC(CO)(CO)N)O
FYR 214.2 Da LogP 2.76 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(c(c2)O)C(=O)O
FZ0 234.2 Da LogP 1.48 TPSA 64.3 ✓ Ro5 ✓ Clean c1cc(cc(c1)OC(F)(F)F)NC(=O)CN
FZ3 220.7 Da LogP 3.17 TPSA 17.8 ✓ Ro5 ✓ Clean c1cc(ccc1CCCn2ccnc2)Cl
FZ6 264.2 Da LogP 0.84 TPSA 84.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)OC(F)(F)F)NC(=O)[C@@H](CO)N
HUM 488.5 Da LogP 2.93 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@](CCN1C=CC(=CC1=O)c2ccc(cc2F)OCc3ccccc3)(C(…
JBA 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 488.5 Da LogP 2.93 TPSA 114.7 ✓ Ro5 ✓ Clean C[C@@](CCN1C=CC(=CC1=O)c2ccc(cc2F)OCc3ccccc3)(C…
JWM 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 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 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 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 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 338.4 Da LogP 1.07 TPSA 98.7 ✓ Ro5 ✓ Clean CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#Cc2ccccc2)O
L63 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 152.1 Da LogP 1.18 TPSA 46.5 ✓ Ro5 ✓ Clean COC(=O)c1ccc(cc1)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.