Protein profile

KP13_00721

Acetylornithine/succinyldiaminopimelate aminotransferase bifunctional protein

Genome: KpKP13

Gene: AHE42339.1 argD Structure source: AlphaFold + ColabFold UniProt A0A0H3H3Z1

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Amino acids 406

Annotations 5

Features 24

PDB binders 6

Druggability 0.552

Overview

Basic information about this protein and its source genome.

Accession: KP13_00721
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42339.1 argD
Status: annotated
Amino acids: 406
Structure source: AlphaFold + ColabFold

GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid. GO:0006525 The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 38.571
Human E-value: 1.07e-07
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 46.134
DEG E-value: 1.26e-114
Localization: Cytoplasmic
ColabFold pLDDT: 97.91

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 0.552

Structure A0A0H3H3Z1

Pocket Pocket 27

P2Rank 0.58

Structure A0A0H3H3Z1

Pocket Pocket 1

ColabFold model

FPocket 0.955 · Pocket 3

P2Rank 0.563 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 156 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
GO:0006525 The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
14	402	PANTHER	PTHR11986	AMINOTRANSFERASE CLASS III
26	400	Pfam	PF00202	Aminotransferase class-III
26	400	InterPro	IPR005814	Aminotransferase class-III
28	157	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
28	157	InterPro	IPR005814	Aminotransferase class-III
173	403	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
173	403	InterPro	IPR005814	Aminotransferase class-III
16	403	Hamap	MF_01107	Acetylornithine/succinyldiaminopimelate aminotransferase [argD].
16	403	InterPro	IPR004636	Acetylornithine/Succinylornithine transaminase family
223	260	ProSitePatterns	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.
223	260	InterPro	IPR005814	Aminotransferase class-III
30	393	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
30	393	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
20	401	SUPERFAMILY	SSF53383	PLP-dependent transferases
20	401	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
60	305	Gene3D	G3DSA:3.40.640.10	-
60	305	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
60	305	FunFam	G3DSA:3.40.640.10:FF:000004	Acetylornithine aminotransferase
17	400	NCBIfam	TIGR00707	acetylornithine/succinylornithine family transaminase
17	400	InterPro	IPR004636	Acetylornithine/Succinylornithine transaminase family
8	404	NCBIfam	TIGR03246	acetylornithine/succinylornithine family transaminase
8	404	InterPro	IPR017652	Acetyl/Succinylornithine transaminase family, bacteria
21	400	CDD	cd00610	OAT_like
21	400	InterPro	IPR005814	Aminotransferase class-III

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_A0A0H3H3Z1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00721	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
3				0.294
1				0.109
28				0.1
18				0.006

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	Score	Probability
1	12.78	0.58
2	11.32	0.522
3	6.62	0.283
4	2.43	0.053
5	2.28	0.047

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
3				0.955
1				0.21

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	Score	Probability
1	8.25	0.44
2	6.38	0.321
3	3.95	0.156
4	2.96	0.096
5	2.2	0.053

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.

57 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
P00	4JEW	P40732	363.3 Da LogP -0.14 TPSA 184.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/OCC[C@@H](C(=O)O)…`
POI	1WKG	Q5SHH5	405.3 Da LogP 0.16 TPSA 178.3	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNCCC[C@@H](C(=O)O)NC(…`
PPE	1WKH	Q5SHH5	379.3 Da LogP -0.47 TPSA 187.8	1 viol.	✓ Clean	`Cc1c(c(c(c[nH+]1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)…`
PXG	4JEV	P40732	368.3 Da LogP 2.02 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNc2cccc(c2)C(=O)O)O`
SUO	4ADD	P77581	232.2 Da LogP -0.84 TPSA 129.7	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)NC(=O)CCC(=O)O)CN`
TNF	4JEW	P40732	229.1 Da LogP 1.12 TPSA 149.7	✓ Ro5	✓ Clean	`c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL330129	P29758	—	127.1 Da LogP -0.19 TPSA 63.3	✓ Ro5	✓ Clean	`C#CC(N)CCC(=O)O`

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
ZINC1883067	1.000	229.1 Da LogP 1.12 TPSA 149.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc([N+](=O)[O-])c(O)c([N+](=O)[O-…`
ZINC2170217	0.792	200.1 Da LogP 0.91 TPSA 126.7	✓ Ro5	Alert	`O=[N+]([O-])c1cc(O)c(O)c([N+](=O)[O-])c1`
ZINC68564159	0.792	366.2 Da LogP 2.40 TPSA 213.0	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(-c2cc([N+](=O)[O-])cc([N+](=O)…`
ZINC34772749	0.769	228.1 Da LogP 0.91 TPSA 143.8	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC1866114950	0.758	260.3 Da LogP -0.06 TPSA 129.7	✓ Ro5	✓ Clean	`NCCCC[C@H](NC(=O)CCCC(=O)O)C(=O)O`
ZINC1555225	0.731	218.6 Da LogP 1.86 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(Cl)c(O)c([N+](=O)[O-])c1`
ZINC1657271	0.731	263.0 Da LogP 1.97 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(Br)c(O)c([N+](=O)[O-])c1`
ZINC34261082	0.731	202.1 Da LogP 1.35 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(F)c(O)c([N+](=O)[O-])c1`
ZINC1530138	0.719	217.3 Da LogP -0.97 TPSA 118.4	✓ Ro5	✓ Clean	`NCCCC[C@H](NC(=O)CCN)C(=O)O`
ZINC15261541	0.706	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC104057557	0.704	378.2 Da LogP 2.26 TPSA 209.9	✓ Ro5	✓ Clean	`O=C(c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1)c1cc([…`
ZINC1530296	0.700	247.2 Da LogP -0.71 TPSA 141.0	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC6783254	0.697	231.2 Da LogP 0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CCCC[C@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC6783285	0.697	231.2 Da LogP 0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CCCC[C@@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC3080634	0.696	200.1 Da LogP 0.91 TPSA 126.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(O)cc([N+](=O)[O-])c1O`
ZINC43450378	0.696	366.2 Da LogP 2.40 TPSA 213.0	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(-c2cc([N+](=O)[O-])c(O)c([N+](…`
ZINC1841206	0.679	212.1 Da LogP 1.02 TPSA 123.6	✓ Ro5	✓ Clean	`O=Cc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC32250330	0.679	214.1 Da LogP 0.70 TPSA 126.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(CO)c(O)c([N+](=O)[O-])c1`
ZINC5956205	0.679	212.2 Da LogP 1.77 TPSA 106.5	✓ Ro5	✓ Clean	`CCc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC100924232	0.667	292.0 Da LogP 2.17 TPSA 129.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc([N+](=O)[O-])c(Br)c([N+](=O)[O…`
ZINC141957116	0.667	342.5 Da LogP 4.00 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@@H](CCCN)C(=O)O`
ZINC1737586	0.667	242.1 Da LogP 1.00 TPSA 132.8	✓ Ro5	✓ Clean	`COC(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC3161143	0.667	255.2 Da LogP 0.91 TPSA 126.8	✓ Ro5	✓ Clean	`CN(C)C(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC3161144	0.667	241.2 Da LogP 0.57 TPSA 135.6	✓ Ro5	✓ Clean	`CNC(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC78044048	0.667	342.5 Da LogP 4.00 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@H](CCCN)C(=O)O`
ZINC1655733	0.655	240.2 Da LogP 2.51 TPSA 106.5	✓ Ro5	✓ Clean	`CC(C)(C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC1687159	0.655	226.2 Da LogP 2.33 TPSA 106.5	✓ Ro5	✓ Clean	`CC(C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC4343573	0.655	214.1 Da LogP 1.22 TPSA 115.7	✓ Ro5	✓ Clean	`COc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC59195086	0.655	242.1 Da LogP 0.84 TPSA 143.8	✓ Ro5	✓ Clean	`O=C(O)Cc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC104179173	0.652	424.2 Da LogP 2.80 TPSA 258.8	1 viol.	✓ Clean	`O=[N+]([O-])c1cc([N+](=O)[O-])c(-c2c([N+](=O)[O…`
ZINC2149898	0.652	216.1 Da LogP 0.62 TPSA 147.0	✓ Ro5	Alert	`O=[N+]([O-])c1cc([N+](=O)[O-])c(O)c(O)c1O`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC1529628	0.649	274.3 Da LogP -1.32 TPSA 165.6	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC3156562	0.645	283.2 Da LogP 1.74 TPSA 135.6	✓ Ro5	✓ Clean	`CC(C)(C)NC(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-]…`
ZINC66139505	0.643	305.2 Da LogP 2.78 TPSA 149.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2cc([N+](=O)[O-])c(O)c([N+]…`
ZINC104122301	0.640	454.2 Da LogP 2.57 TPSA 282.9	1 viol.	✓ Clean	`O=[N+]([O-])c1cc([N+](=O)[O-])c(NNc2c([N+](=O)[…`
ZINC1693336	0.640	218.6 Da LogP 1.86 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(Cl)cc([N+](=O)[O-])c1O`
ZINC1706150	0.640	202.1 Da LogP 1.35 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(F)cc([N+](=O)[O-])c1O`
ZINC34328127	0.640	263.0 Da LogP 1.97 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(Br)cc([N+](=O)[O-])c1O`
ZINC5113904	0.639	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`NCCC[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)O`
ZINC147300883	0.636	217.2 Da LogP 0.22 TPSA 103.7	✓ Ro5	✓ Clean	`CCC[C@@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC24803120	0.636	217.2 Da LogP 0.22 TPSA 103.7	✓ Ro5	✓ Clean	`CCC[C@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC100006785	0.630	256.1 Da LogP 0.51 TPSA 172.5	✓ Ro5	✓ Clean	`NC(=O)c1c([N+](=O)[O-])cc([N+](=O)[O-])cc1[N+](…`
ZINC116981435	0.629	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC116981437	0.629	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC116981440	0.629	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC40860752	0.629	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)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.