Protein target profile

KP13_04607

4-hydroxy-2-oxovalerate aldolase

Genome: KpKP13 Gene: mhpE AHE44133.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GU24

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Length 338

Pocket druggability 0.032

Direct ligand evidence 0 51 total records

Functional annotation 1 EC 8 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

Second pocket predictor agrees P2Rank predicted binding-site probability 0.60. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 5 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 (%): 26.515 Lower values reduce human off-target concern.
Human E-value: 5.31e-07
Gut microbiome similarity: 1.1% 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: 98.05 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 0.032

Structure A0A0H3GU24

Pocket Pocket 2

P2Rank 0.6

Structure A0A0H3GU24

Pocket Pocket 1

ColabFold model

FPocket 0.684 · Pocket 21

P2Rank 0.343 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 50 / 4744 genomes with a hit

Prevalence 1.1%

Cross-references

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

Sequence

UniProt A0A0H3GU24

Sequence

Primary amino-acid sequence viewer.

MNGKKLYISDVTLRDGMHAIRHQYSLAQVQQIAGALDKAGVDSIEVAHGDGLQGSSFNYGFGAHSDIAWIEAAADVVSQAKIATLLLPGIGTLHDLKAAYQAGARVVRVATHCSEADVAAQHIAFARELGMDTVGFLMMSHMISPQALAQQALKMESYGATCIYVVDSGGAMNMNDIRDRFRALKAVLKPETATGMHAHHNLSLGVANSIVAVEEGCDRIDASLAGMGAGAGNAPLEVFIVAADKLGWQHGTDLYALMNAADELVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEAAAKRYGLSAVDILVELGKRRMVGGQEDMIVDVALDLLNRNK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

4.1.3.39

Gene Ontology (GO)

GO:0019439 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
GO:0016833 Catalysis of the cleavage of a C-C bond by other means than by hydrolysis or oxidation, of a 3-hydroxy 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:0008701 Catalysis of the reaction: 4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate.
GO:0003852 Catalysis of the reaction: 3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H+.
GO:0030145 Binding to a manganese ion (Mn).
GO:0019380 The chemical reactions and pathways resulting in the breakdown of 3-phenylpropionate, the anion of phenylpropanoic acid.
GO:0009098 The chemical reactions and pathways resulting in the formation of L-leucine, 2-amino-4-methylpentanoic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
4	255	PANTHER	PTHR10277	HOMOCITRATE SYNTHASE-RELATED
6	258	ProSiteProfiles	PS50991	Pyruvate carboxyltransferase domain.
6	258	InterPro	IPR000891	Pyruvate carboxyltransferase
4	336	NCBIfam	TIGR03217	4-hydroxy-2-oxovalerate aldolase
4	336	InterPro	IPR017629	4-hydroxy-2-oxovalerate aldolase
275	337	FunFam	G3DSA:1.10.8.60:FF:000042	4-hydroxy-2-oxovalerate aldolase
3	276	SUPERFAMILY	SSF51569	Aldolase
2	268	Gene3D	G3DSA:3.20.20.70	Aldolase class I
2	268	InterPro	IPR013785	Aldolase-type TIM barrel
6	269	CDD	cd07943	DRE_TIM_HOA
6	269	InterPro	IPR035685	4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain
1	338	Hamap	MF_01656	4-hydroxy-2-oxovalerate aldolase [mhpE].
1	338	InterPro	IPR017629	4-hydroxy-2-oxovalerate aldolase
275	338	Gene3D	G3DSA:1.10.8.60	-
288	336	SUPERFAMILY	SSF89000	post-HMGL domain-like
6	262	Pfam	PF00682	HMGL-like
6	262	InterPro	IPR000891	Pyruvate carboxyltransferase
274	333	Pfam	PF07836	DmpG-like communication domain
274	333	InterPro	IPR012425	DmpG-like communication

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 · P2Rank

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

Site 1 P2Rank #1

0.6

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Surrounding area

Site 2 P2Rank #2

0.411

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Surrounding area

Site 3 P2Rank #3

0.081

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Surrounding area

Site 4 P2Rank #4

0.015

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Surrounding area

Residue sets

UniProt: Active site:8-8 Proton acceptor

UniProt: Binding site:158-158

UniProt: Binding site:187-187

UniProt: Binding site:189-189

UniProt: Binding site:278-278

UniProt: Binding site:4-5

UniProt: Binding site:5-5

UniProt: Site:4-4 Transition state stabilizer

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.343

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Surrounding area

Site 2 P2Rank #2

0.078

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Surrounding area

Site 3 P2Rank #3

0.033

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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_A0A0H3GU24	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04607	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.

51 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 46 similarity-based ZINC candidates

Best available ligand signal

FOR PDB via homolog 30.0 Da · LogP -0.18 · TPSA 17.1 Open detail RCSB PDB

KMT PDB via homolog Detail RCSB PDB

MLI PDB via homolog Detail RCSB PDB

OXL PDB via homolog Detail RCSB PDB

PYR 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
FOR RCSB PDB	4LRS	D1A3K8	30.0 Da LogP -0.18 TPSA 17.1	✓ Ro5	✓ Clean	`C=O`
KMT RCSB PDB	6E1J	C5J4P1	148.2 Da LogP 0.39 TPSA 54.4	✓ Ro5	✓ Clean	`CSCCC(=O)C(=O)O`
MLI RCSB PDB	3BLE	Q8F3Q1	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
OXL RCSB PDB	1NVM	P51016	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
PYR RCSB PDB	4LRS	D1A3K8	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=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
ZINC2384798 ZINC	0.607	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC2391059 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)O)[C@@H](C)CC`
ZINC40472549 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](C(=O)O)[C@@H](C)…`
ZINC40490721 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@@H](N)[C@H](C)CC)C(=O…`
ZINC5909388 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@@H](N)[C@H](C)CC)C(=O)O`
ZINC4899467 ZINC	0.567	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC5662848 ZINC	0.567	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC5662849 ZINC	0.567	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC5662850 ZINC	0.567	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC255963942 ZINC	0.548	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…`
ZINC255963943 ZINC	0.548	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…`
ZINC2560984 ZINC	0.548	246.3 Da LogP -0.60 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC2575119 ZINC	0.548	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC39831468 ZINC	0.548	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…`
ZINC4762961 ZINC	0.548	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…`
ZINC13529436 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC19502834 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502836 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502838 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC13508097 ZINC	0.531	234.3 Da LogP -0.14 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](CS)C(=O)O`
ZINC2556613 ZINC	0.531	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)O`
ZINC11959312 ZINC	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCN(C)CC1`
ZINC11959315 ZINC	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCN(C)CC1`
ZINC19504598 ZINC	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCN(C)CC1`
ZINC19504599 ZINC	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCN(C)CC1`
ZINC2390958 ZINC	0.516	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@@H](N)C(C)C)C(=O)O`
ZINC40472548 ZINC	0.516	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](NC(=O)[C@@H](N)C(C)C)C(=O)O`
ZINC8577168 ZINC	0.516	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@@H](N)C(C)C)C(=O)O`
ZINC2522618 ZINC	0.515	245.3 Da LogP -1.20 TPSA 135.5	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](CC(N)=O)C(=O)O`
ZINC11959285 ZINC	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCOCC1`
ZINC11959288 ZINC	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCOCC1`
ZINC1575515 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC19506206 ZINC	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCOCC1`
ZINC19506207 ZINC	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCOCC1`
ZINC2384845 ZINC	0.500	260.3 Da LogP -0.21 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC2545171 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC25624992 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](NC(=O)[C@H](C)N)C(=O)O`
ZINC25625001 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](NC(=O)[C@H](C)N)C(=O)O`
ZINC36158109 ZINC	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)OCc1ccccc1`
ZINC36158113 ZINC	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)OCc1ccccc1`
ZINC37246007 ZINC	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)OCc1ccccc1`
ZINC37246008 ZINC	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)OCc1ccccc1`
ZINC4787494 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC4787500 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC4899420 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@H](C)N)C(=O)O`
ZINC8577157 ZINC	0.500	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@H](C)N)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.

KP13_04607

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

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence