Protein profile

KP13_01800

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

Genome: KpKP13

Gene: AHE46240.1 lpxD Structure source: AlphaFold + ColabFold UniProt A0A0H3GS43

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Amino acids 341

Annotations 7

Features 28

PDB binders 18

Druggability 0.707

Overview

Basic information about this protein and its source genome.

Accession: KP13_01800
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46240.1 lpxD
Status: annotated
Amino acids: 341
Structure source: AlphaFold + ColabFold

2.3.1.191

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+.

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 (%): 93.842
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.37

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 0.707

Structure A0A0H3GS43

Pocket Pocket 1

P2Rank 0.122

Structure A0A0H3GS43

Pocket Pocket 1

ColabFold model

FPocket 0.479 · Pocket 5

P2Rank 0.158 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 159 / 4744 genomes with a hit

Normalized 0.034

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)

2.3.1.191

Gene Ontology (GO)

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

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_A0A0H3GS43	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01800	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
1				0.707
7				0.465
10				0.239

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
5				0.479

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

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.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
1F7	4IHF	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	4IHG	P21645	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](CC(=O)O)O`
O3V	6P84	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	6P83	P21645	417.9 Da LogP 5.60 TPSA 68.0	1 viol.	✓ Clean	`CC1(Cc2c(c(c3c(n2)nn(c3O)c4ccccc4)c5ccccc5Cl)C(…`
O4D	6P8A	P21645	396.5 Da LogP 1.68 TPSA 77.2	✓ Ro5	✓ Clean	`Cc1cc(nc2c1c(nn2CC(=O)NCCCN3CCOCC3)n4cccc4)C`
O4G	6P88	P21645	364.4 Da LogP 3.56 TPSA 89.8	✓ Ro5	✓ Clean	`c1cc(cc(c1)NC(=O)c2ccco2)NC(=O)c3ccc4c(c3)OCCO4`
O4P	6P87	P21645	406.5 Da LogP 4.86 TPSA 54.6	✓ Ro5	✓ Clean	`CN([C@@H](c1cccs1)c2c[nH]c3c2cccc3)C(=O)COc4ccc…`
O4S	6P86	P21645	474.6 Da LogP 3.51 TPSA 73.0	✓ Ro5	✓ Clean	`CCc1ccc(cc1)CNC(=O)CN2c3cc(ccc3N4CCCC[C@@H]4C2=…`
O4V	6P85	P21645	358.4 Da LogP 2.39 TPSA 100.1	✓ Ro5	✓ Clean	`CCOc1ccccc1n2c(c(nn2)S(=O)(=O)c3ccc(cc3)C)N`
PE5	4R36	Q5LH16	398.5 Da LogP 0.13 TPSA 94.1	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCOCCO`
PG0	4R36	Q5LH16	120.1 Da LogP -0.36 TPSA 38.7	✓ Ro5	✓ Clean	`COCCOCCO`
PNS	4IHG	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	6OSS	B4F258	79.0 Da LogP -1.64 TPSA 63.2	✓ Ro5	✓ Clean	`[O-][P-](=O)[O-]`
Q5M	6UEC	Q9HXY6	228.2 Da LogP 2.89 TPSA 54.4	✓ Ro5	✓ Clean	`c1ccc2c(c1)cccc2C(=O)CCC(=O)O`
S2N	3I3A	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	3I3X	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	4R37	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	7OKB	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…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC100305273	1.000	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](O)CC(=O)O`
ZINC100305277	1.000	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC100500540	1.000	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC100500548	1.000	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](O)CC(=O)O`
ZINC100500553	1.000	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC15835555	1.000	406.5 Da LogP 4.86 TPSA 54.6	✓ Ro5	✓ Clean	`COc1ccccc1OCC(=O)N(C)[C@@H](c1cccs1)c1c[nH]c2cc…`
ZINC15835557	1.000	406.5 Da LogP 4.86 TPSA 54.6	✓ Ro5	✓ Clean	`COc1ccccc1OCC(=O)N(C)[C@H](c1cccs1)c1c[nH]c2ccc…`
ZINC16051927	1.000	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](O)CC(=O)O`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC2039068	1.000	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](O)CC(=O)O`
ZINC2039069	1.000	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC236510	1.000	228.2 Da LogP 2.89 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1cccc2ccccc12`
ZINC2504625	1.000	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](O)CC(=O)O`
ZINC2558055	1.000	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCC[C@H](O)CC(=O)O`
ZINC2558056	1.000	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](O)CC(=O)O`
ZINC32838984	1.000	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC32838986	1.000	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC[C@H](O)CC(=O)O`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC6817538	1.000	358.4 Da LogP 2.39 TPSA 100.1	✓ Ro5	✓ Clean	`CCOc1ccccc1-n1nnc(S(=O)(=O)c2ccc(C)cc2)c1N`
ZINC754049	1.000	364.4 Da LogP 3.56 TPSA 89.8	✓ Ro5	✓ Clean	`O=C(Nc1cccc(NC(=O)c2ccco2)c1)c1ccc2c(c1)OCCO2`
ZINC85915165	1.000	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)CC(=O)O`
ZINC2858547	0.864	350.3 Da LogP 3.51 TPSA 89.8	✓ Ro5	✓ Clean	`O=C(Nc1cccc(NC(=O)c2ccco2)c1)c1ccc2c(c1)OCO2`
ZINC861606	0.860	364.4 Da LogP 3.56 TPSA 89.8	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2ccco2)cc1)c1ccc2c(c1)OCCO2`
ZINC8907957	0.844	364.4 Da LogP 3.56 TPSA 89.8	✓ Ro5	✓ Clean	`O=C(Nc1ccc2c(c1)OCCO2)c1cccc(NC(=O)c2ccco2)c1`
ZINC2378696	0.828	242.3 Da LogP 3.28 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1cccc2ccccc12`
ZINC2378697	0.800	256.3 Da LogP 3.67 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1cccc2ccccc12`
ZINC8060160	0.800	364.4 Da LogP 3.56 TPSA 89.8	✓ Ro5	✓ Clean	`O=C(Nc1ccc2c(c1)OCCO2)c1ccc(NC(=O)c2ccco2)cc1`
ZINC15835570	0.789	406.5 Da LogP 4.86 TPSA 54.6	✓ Ro5	✓ Clean	`COc1ccc(OCC(=O)N(C)[C@@H](c2cccs2)c2c[nH]c3cccc…`
ZINC15835572	0.789	406.5 Da LogP 4.86 TPSA 54.6	✓ Ro5	✓ Clean	`COc1ccc(OCC(=O)N(C)[C@H](c2cccs2)c2c[nH]c3ccccc…`
ZINC15835539	0.786	376.5 Da LogP 4.86 TPSA 45.3	✓ Ro5	✓ Clean	`CN(C(=O)COc1ccccc1)[C@@H](c1cccs1)c1c[nH]c2cccc…`
ZINC15835541	0.786	376.5 Da LogP 4.86 TPSA 45.3	✓ Ro5	✓ Clean	`CN(C(=O)COc1ccccc1)[C@H](c1cccs1)c1c[nH]c2ccccc…`
ZINC15835551	0.783	421.5 Da LogP 4.76 TPSA 88.5	✓ Ro5	✓ Clean	`CN(C(=O)COc1ccccc1[N+](=O)[O-])[C@@H](c1cccs1)c…`
ZINC15835553	0.783	421.5 Da LogP 4.76 TPSA 88.5	✓ Ro5	✓ Clean	`CN(C(=O)COc1ccccc1[N+](=O)[O-])[C@H](c1cccs1)c1…`
ZINC31159540	0.778	204.3 Da LogP 1.15 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)C[C@@H](O)CC(=O)O`
ZINC31159544	0.778	204.3 Da LogP 1.15 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)C[C@@H](O)CC(=O)O`
ZINC31159548	0.778	204.3 Da LogP 1.15 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)C[C@H](O)CC(=O)O`
ZINC31159552	0.778	204.3 Da LogP 1.15 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)C[C@H](O)CC(=O)O`
ZINC15835543	0.776	394.5 Da LogP 5.00 TPSA 45.3	✓ Ro5	✓ Clean	`CN(C(=O)COc1ccc(F)cc1)[C@@H](c1cccs1)c1c[nH]c2c…`
ZINC15835545	0.776	394.5 Da LogP 5.00 TPSA 45.3	✓ Ro5	✓ Clean	`CN(C(=O)COc1ccc(F)cc1)[C@H](c1cccs1)c1c[nH]c2cc…`
ZINC2243634	0.774	284.4 Da LogP 4.45 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)c1cccc2ccccc12`
ZINC2378699	0.774	270.3 Da LogP 4.06 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)c1cccc2ccccc12`
ZINC8610730	0.769	460.6 Da LogP 3.25 TPSA 73.0	✓ Ro5	✓ Clean	`Cc1cccc(CNC(=O)CN2C(=O)[C@@H]3CCCCN3c3ccc(C(=O)…`
ZINC147022	0.767	245.2 Da LogP 2.30 TPSA 60.7	✓ Ro5	✓ Clean	`O=C(Nc1ccc2c(c1)OCCO2)c1ccco1`

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.