Protein profile

KP13_04991

Succinylornithine transaminase

Genome: KpKP13

Gene: AHE44834.1 astC Structure source: AlphaFold + ColabFold UniProt A0A0H3GP38

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Amino acids 401

Annotations 13

Features 24

PDB binders 7

Druggability 0.695

Overview

Basic information about this protein and its source genome.

Accession: KP13_04991
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44834.1 astC
Status: annotated
Amino acids: 401
Structure source: AlphaFold + ColabFold

2.6.1.11 2.6.1.17

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. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.286
Human E-value: 2.45e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 45.918
DEG E-value: 1.4999999999999999e-105
Localization: Unknown
ColabFold pLDDT: 97.95

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 0.695

Structure A0A0H3GP38

Pocket Pocket 1

P2Rank 0.529

Structure A0A0H3GP38

Pocket Pocket 1

ColabFold model

FPocket 0.453 · Pocket 15

P2Rank 0.442 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 167 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 11 GO

Enzyme Commission (EC)

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.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0042802 Binding to an identical protein or proteins.
GO:0003992 Catalysis of the reaction: N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate.
GO:0009016 Catalysis of the reaction: N-succinyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2-succinylamino-6-oxoheptanedioate + L-glutamate.
GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
26	155	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
26	155	InterPro	IPR005814	Aminotransferase class-III
169	399	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
169	399	InterPro	IPR005814	Aminotransferase class-III
57	301	Gene3D	G3DSA:3.40.640.10	-
57	301	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
16	397	SUPERFAMILY	SSF53383	PLP-dependent transferases
16	397	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
220	257	ProSitePatterns	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.
220	257	InterPro	IPR005814	Aminotransferase class-III
13	399	Hamap	MF_01107	Acetylornithine/succinyldiaminopimelate aminotransferase [argD].
13	399	InterPro	IPR004636	Acetylornithine/Succinylornithine transaminase family
9	397	PANTHER	PTHR11986	AMINOTRANSFERASE CLASS III
14	396	NCBIfam	TIGR00707	acetylornithine/succinylornithine family transaminase
14	396	InterPro	IPR004636	Acetylornithine/Succinylornithine transaminase family
6	399	NCBIfam	TIGR03246	acetylornithine/succinylornithine family transaminase
6	399	InterPro	IPR017652	Acetyl/Succinylornithine transaminase family, bacteria
18	396	CDD	cd00610	OAT_like
18	396	InterPro	IPR005814	Aminotransferase class-III
57	302	FunFam	G3DSA:3.40.640.10:FF:000004	Acetylornithine aminotransferase
27	388	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
27	388	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
23	395	Pfam	PF00202	Aminotransferase class-III
23	395	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_A0A0H3GP38	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04991	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				0.695

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	6.31	0.317
3	2.54	0.071
4	1.71	0.03
5	1.63	0.026

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
15				0.453
11				0.422

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	5.7	0.276
2	5.52	0.264
3	3.62	0.135
4	1.49	0.021

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)…`
PUT	4UOX	P42588	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
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).

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
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-…`
ZINC1685531	0.875	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707	0.875	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646	0.875	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
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`

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.