Protein target profile

KP13_05467

Diaminobutyrate--2-oxoglutarate aminotransferase

Genome: KpKP13 Gene: AHE44472.1 dat 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXZ5

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Length 461

Pocket druggability 0.578

Direct ligand evidence 0 43 total records

Functional annotation 0 EC 4 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.58. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 8 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Human identity (%): 29.736 Lower values reduce human off-target concern.
Human E-value: 1.38e-39
Gut microbiome similarity: 2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 95.57 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.578

Structure A0A0H3GXZ5

Pocket Pocket 29

P2Rank 0.379

Structure A0A0H3GXZ5

Pocket Pocket 1

ColabFold model

FPocket 0.593 · Pocket 6

P2Rank 0.445 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 96 / 4744 genomes with a hit

Prevalence 2.0%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GXZ5

Sequence

Primary amino-acid sequence viewer.

MMTDKVRIDTLRADLLDANNETFLARQAEFESNVRSYPRKLPLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTTPLKDRFSEYLLSCLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRTAVISFSGGYHGMTHGALSVTGNLSPKAAVNGMMPEVQFMPYPHLYRCPLGIGGEAGVKALTYYFENLINDVESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTEEHGILLIVDEVQAGFARTGKFFAFEHAGIQPDIIVMSKAVGGGLPLAVLGIKKQFDAWEPGHHTGTFRGNQLAMATGLTTLRHLRDNKIADKVAAQGEWLKGKLAELQKRYPVIGHVRGLGLMIGIEIVKPNEAQDHMGCYPADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISDAELDVFLDKFEQALLAAGVKPV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 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: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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
24	149	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
24	149	InterPro	IPR005814	Aminotransferase class-III
142	456	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
142	456	InterPro	IPR005814	Aminotransferase class-III
31	450	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
31	450	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
21	455	PANTHER	PTHR43552	DIAMINOBUTYRATE--2-OXOGLUTARATE AMINOTRANSFERASE
21	455	InterPro	IPR004637	2,4-diaminobutyrate 4-transaminase
263	300	ProSitePatterns	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.
263	300	InterPro	IPR005814	Aminotransferase class-III
31	453	SUPERFAMILY	SSF53383	PLP-dependent transferases
31	453	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
24	453	CDD	cd00610	OAT_like
24	453	InterPro	IPR005814	Aminotransferase class-III
40	453	Pfam	PF00202	Aminotransferase class-III
40	453	InterPro	IPR005814	Aminotransferase class-III
77	344	Gene3D	G3DSA:3.40.640.10	-
77	344	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
77	345	FunFam	G3DSA:3.40.640.10:FF:000004	Acetylornithine aminotransferase
22	455	NCBIfam	TIGR00709	diaminobutyrate--2-oxoglutarate transaminase family protein
22	455	InterPro	IPR004637	2,4-diaminobutyrate 4-transaminase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #29

0.578

Likely same site as P2Rank 2 1.2 Å 11 shared residues 100% of smaller site

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.379

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Surrounding area

Site 2 P2Rank #2

0.31

Likely same site as FPocket 29 1.2 Å 11 shared residues 100% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.052

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Surrounding area

Site 4 P2Rank #4

0.041

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Surrounding area

Site 5 P2Rank #5

0.039

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.445

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Surrounding area

Site 2 P2Rank #2

0.335

Likely same site as FPocket 6 1.9 Å 12 shared residues 92% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.058

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Surrounding area

Site 4 P2Rank #4

0.034

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Surrounding area

Site 5 P2Rank #5

0.029

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Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GXZ5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05467	ColabFold	—	—	full sequence	—	Loaded

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.

43 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 35 similarity-based ZINC candidates

Best available ligand signal

7VO PDB via homolog 362.3 Da · LogP 1.29 · TPSA 149.2 Open detail RCSB PDB

IK2 PDB via homolog Detail RCSB PDB

ILP PDB via homolog Detail RCSB PDB

PMP PDB via homolog Detail RCSB PDB

POI PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
7VO RCSB PDB	5WYA	M1GRN3	362.3 Da LogP 1.29 TPSA 149.2	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)…`
IK2 RCSB PDB	1SFF	P22256	322.2 Da LogP -0.19 TPSA 158.4	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNOCC(=O)O)O`
ILP RCSB PDB	5WYF	M1GRN3	362.3 Da LogP 1.29 TPSA 149.2	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(…`
PMP RCSB PDB	1SZK	P22256	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN)O`
POI RCSB PDB	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 RCSB PDB	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 RCSB PDB	4UOX	P42588	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
TAR RCSB PDB	6WOP	D0CCF6	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@@H](C(=O)O)O)(C(=O)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
ZINC1532708 ZINC	1.000	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC1685531 ZINC	0.875	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707 ZINC	0.875	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646 ZINC	0.875	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
ZINC1532705 ZINC	0.769	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC12359024 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1656021 ZINC	0.692	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC2013424 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532514 ZINC	0.643	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC1560405156 ZINC	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157 ZINC	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC13377742 ZINC	0.538	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1545440 ZINC	0.538	213.4 Da LogP 4.65 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCN`
ZINC2385445 ZINC	0.538	201.4 Da LogP 2.84 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCO`
ZINC34196183 ZINC	0.538	229.4 Da LogP 3.62 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCO`
ZINC38585283 ZINC	0.538	203.4 Da LogP 3.39 TPSA 26.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCS`
ZINC38684714 ZINC	0.538	230.4 Da LogP 0.51 TPSA 81.3	✓ Ro5	✓ Clean	`NCCCCN(CCCCN)CCCCN`
ZINC1529994 ZINC	0.523	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC2114966 ZINC	0.519	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC13213450 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@H](C(=O)O)CS2)c…`
ZINC13213453 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@H](C(=O)O)CS2)c1O`
ZINC13213455 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@@H](C(=O)O)CS2)…`
ZINC13213457 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@@H](C(=O)O)CS2)c…`
ZINC1529331 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529332 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1529333 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529334 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1598087 ZINC	0.500	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`

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.