Protein profile

VK055_3228

acetylglutamate kinase

Genome: KpATCC43816

Gene: argB AIK81789.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPQ8

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Amino acids 257

Annotations 6

Features 16

PDB binders 20

Druggability 0.386

Overview

Basic information about this protein and its source genome.

Accession: VK055_3228
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: argB AIK81789.1
Status: annotated
Amino acids: 257
Structure source: AlphaFold + ColabFold

2.7.2.8

GO:0003991 Catalysis of the reaction: ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate-5-phosphate. GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0042450 OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 33.992
Localization: Cytoplasmic
ColabFold pLDDT: 95.12

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 0.386

Structure A0A0H3GPQ8

Pocket Pocket 2

P2Rank 0.888

Structure A0A0H3GPQ8

Pocket Pocket 1

ColabFold model

FPocket 0.288 · Pocket 3

P2Rank 0.907 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 129 / 4744 genomes with a hit

Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

2.7.2.8

Gene Ontology (GO)

GO:0003991 Catalysis of the reaction: ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate-5-phosphate.
GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0042450 OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
4	255	CDD	cd04249	AAK_NAGK-NC
4	255	InterPro	IPR041731	N-Acetyl-L-glutamate kinase, noncyclic
1	257	FunFam	G3DSA:3.40.1160.10:FF:000008	Acetylglutamate kinase
4	255	PANTHER	PTHR23342	N-ACETYLGLUTAMATE SYNTHASE
1	250	Hamap	MF_00082	Acetylglutamate kinase [argB].
1	250	InterPro	IPR037528	Acetylglutamate kinase ArgB
4	234	Pfam	PF00696	Amino acid kinase family
4	234	InterPro	IPR001048	Aspartate/glutamate/uridylate kinase
2	255	SUPERFAMILY	SSF53633	Carbamate kinase-like
2	255	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
1	257	PIRSF	PIRSF000728	NAGK
1	257	InterPro	IPR004662	Acetylglutamate kinase family
1	257	Gene3D	G3DSA:3.40.1160.10	-
1	257	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
4	233	NCBIfam	TIGR00761	acetylglutamate kinase
4	233	InterPro	IPR004662	Acetylglutamate kinase family

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_A0A0H3GPQ8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3228	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				0.386
4				0.018
3				0.001
12				0.0

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				28.23	0.888
2				1.94	0.033

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
10				0.223
7				0.006
1				0.001
6				0.0

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				30.99	0.907
2				1.79	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.

70 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
14N	7NLT	P9WQ01	220.3 Da LogP 1.14 TPSA 43.8	✓ Ro5	✓ Clean	`CN1CCN(CC1)c2ccc(cc2)C(=O)O`
5RN	7NLU	P9WQ01	159.2 Da LogP 2.37 TPSA 32.9	✓ Ro5	✓ Clean	`CC(=O)c1c[nH]c2c1cccc2`
97Q	7NNB	P9WQ01	281.2 Da LogP 3.98 TPSA 33.1	✓ Ro5	✓ Clean	`c1cc2c(cc(nc2c(c1)C(F)(F)F)C(F)(F)F)O`
97T	7NLQ	P9WQ01	161.2 Da LogP 2.05 TPSA 46.3	✓ Ro5	✓ Clean	`c1ccc(c(c1)c2ccno2)O`
97W	7NLX	P9WQ01	213.2 Da LogP 2.96 TPSA 33.1	✓ Ro5	✓ Clean	`c1cc2c(ccnc2cc1C(F)(F)F)O`
98K	7NLY	P9WQ01	152.6 Da LogP 2.22 TPSA 28.7	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c(n2)Cl`
98Q	7NLZ	P9WQ01	215.2 Da LogP 3.20 TPSA 25.0	✓ Ro5	✓ Clean	`COc1cc2cc[nH]c2cc1C(F)(F)F`
98T	7NLS	P9WQ01	278.0 Da LogP 1.78 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(c(c1)I)O`
98W	7NN7	P9WQ01	210.2 Da LogP 0.97 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)c1cc(cc(c1)O)C(=O)OC`
98Z	7NN8	P9WQ01	142.2 Da LogP 2.04 TPSA 39.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C#N`
9EQ	7NM0	P9WQ01	152.1 Da LogP 1.30 TPSA 57.5	✓ Ro5	✓ Clean	`CC(=O)c1c(cccc1O)O`
ANP	1GS5	P0A6C8	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)…`
DTU	2WXB	P0A6C8	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@H]([C@H](CS)O)O)S`
GGB	7NLP	P9WQ01	176.2 Da LogP -1.80 TPSA 134.5	✓ Ro5	✓ Clean	`[H]/N=C(\N)/NOCC[C@@H](C(=O)O)N`
NHE	7NLO	P9WQ01	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
NLG	1GS5	P0A6C8	189.2 Da LogP -0.56 TPSA 103.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CCC(=O)O)C(=O)O`
PIY	7NLR	P9WQ01	144.2 Da LogP 2.08 TPSA 28.7	✓ Ro5	✓ Clean	`c1ccc(cc1)c2[nH]ccn2`
SRT	3T7B	Q8ZA87	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@H](C(=O)O)O)(C(=O)O)O`
UOK	7NLW	P9WQ01	186.2 Da LogP 2.24 TPSA 48.8	✓ Ro5	✓ Clean	`COc1ccc2c(c1)c(c[nH]2)CC#N`
X2W	2X2W	P0A6C8	269.1 Da LogP -1.01 TPSA 150.2	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CCC(=O)OP(=O)(O)O)C(=O)O`

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
ZINC158905	1.000	220.3 Da LogP 1.14 TPSA 43.8	✓ Ro5	✓ Clean	`CN1CCN(c2ccc(C(=O)O)cc2)CC1`
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC2548331	1.000	278.0 Da LogP 1.78 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(O)c(I)c1`
ZINC32327	1.000	210.2 Da LogP 0.97 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)c1cc(O)cc(C(=O)OC)c1`
ZINC34503706	1.000	215.2 Da LogP 3.20 TPSA 25.0	✓ Ro5	✓ Clean	`COc1cc2cc[nH]c2cc1C(F)(F)F`
ZINC8830538	1.000	281.2 Da LogP 3.98 TPSA 33.1	✓ Ro5	✓ Clean	`Oc1cc(C(F)(F)F)nc2c(C(F)(F)F)cccc12`
ZINC89202735	0.913	220.3 Da LogP 3.74 TPSA 28.7	✓ Ro5	✓ Clean	`c1ccc(-c2ccc(-c3ncc[nH]3)cc2)cc1`
ZINC12370640	0.862	234.3 Da LogP 1.53 TPSA 43.8	✓ Ro5	✓ Clean	`CN1CCCN(c2ccc(C(=O)O)cc2)CC1`
ZINC1532510	0.821	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CCC(=O)O)C(=…`
ZINC1532511	0.821	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CC(=O)O)C(=O)N[C@@H](CCC(=O)O)C(=O…`
ZINC1532512	0.821	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC(=O)O)C(=O)N[C@H](CCC(=O)O)C(=O…`
ZINC1532513	0.821	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CC(=O)O)C(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC12360002	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC56412	0.800	252.2 Da LogP 1.05 TPSA 78.9	✓ Ro5	✓ Clean	`COC(=O)c1cc(C(=O)OC)cc(C(=O)OC)c1`
ZINC2504638	0.793	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=…`
ZINC4534089	0.793	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O…`
ZINC4534090	0.793	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O…`
ZINC4534091	0.793	304.3 Da LogP -1.60 TPSA 170.1	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC169847	0.759	218.3 Da LogP 1.64 TPSA 23.6	✓ Ro5	✓ Clean	`CC(=O)c1ccc(N2CCN(C)CC2)cc1`
ZINC15923743	0.743	227.2 Da LogP 3.27 TPSA 33.1	✓ Ro5	✓ Clean	`Cc1cccc2c(O)cc(C(F)(F)F)nc12`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC2560824	0.733	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC82264502	0.733	219.3 Da LogP 0.54 TPSA 49.6	✓ Ro5	✓ Clean	`CN1CCN(c2ccc(C(N)=O)cc2)CC1`
ZINC8700304	0.733	278.0 Da LogP 1.78 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(I)c(O)c1`
ZINC58123315	0.731	376.3 Da LogP -1.36 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@H](NC(=O)CCC(=O)N[C@@H](CCC(=O)O)C(=…`
ZINC58123326	0.731	376.3 Da LogP -1.36 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@@H](NC(=O)CCC(=O)N[C@H](CCC(=O)O)C(=…`

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.