Protein target profile

KP13_05015

Fumarate hydratase class I, aerobic

Genome: KpKP13 Gene: AHE44810.1 fumA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GP67

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Length 548

Pocket druggability 0.412

Direct ligand evidence 0 47 total records

Functional annotation 1 EC 8 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

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: No hit
Gut microbiome similarity: 15.4% 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: 96.34 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 0.412

Structure A0A0H3GP67

Pocket Pocket 20

P2Rank 0.817

Structure A0A0H3GP67

Pocket Pocket 1

ColabFold model

FPocket 0.63 · Pocket 3

P2Rank 0.777 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 731 / 4744 genomes with a hit

Prevalence 15.4%

Cross-references

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

Sequence

UniProt A0A0H3GP67

Sequence

Primary amino-acid sequence viewer.

MSNKPFVYQDPFPLKKDDTEYYLLSSDYVSVAEFAGQEVLKVDPQALTLLAQHAFHDASFMLRPAHQQQVADILNDPEASENDKYVALQFLRNSDIAAKGILPTCQDTGTAIIMGKKGQRVWTGGGDEAALAQGVYNTYIQDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYATDGDEYKFLCIAKGGGSANKTYLYQETKALITPAKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAEATLKTVKLASTKYYDGLPTEGNEHGQAFRDVQLEQELLLEAQNLGLGAQFGGKYFAHDIRVIRLPRHGASCPVGMGVSCSADRNIKAKINRDGIWLEKLESNPGKYIPEHLRQAGEGEAVKVNLNQPMSEILAQLSQYPVSTRLSLSGTIIVARDIAHAKLKELIDNGEALPQYVKDHPIYYAGPAKTPDGYASGSLGPTTAGRMDSYVDLLQSHGASKIMLAKGNRSQQVTDACHKHGGFYLGSIGGPAAVLAQQSIKSLECVAYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQIQTSQCARCVK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

4.2.1.2

Gene Ontology (GO)

GO:0006091 The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
GO:0004333 Catalysis of the reaction: (S)-malate = fumarate + H2O.
GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0046872 Binding to a metal ion.
GO:0042803 Binding to an identical protein to form a homodimer.
GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
347	537	Gene3D	G3DSA:3.20.130.10	-
347	537	InterPro	IPR036660	Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily
373	537	NCBIfam	TIGR00723	FumA C-terminus/TtdB family hydratase beta subunit
373	537	InterPro	IPR004647	Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain
347	537	FunFam	G3DSA:3.20.130.10:FF:000001	Fumarate hydratase class I
362	536	SUPERFAMILY	SSF117457	FumA C-terminal domain-like
362	536	InterPro	IPR036660	Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily
332	537	Pfam	PF05683	Fumarase C-terminus
332	537	InterPro	IPR004647	Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain
30	548	PIRSF	PIRSF001394	Fe_dep_fumar_hy
30	548	InterPro	IPR011167	Iron-dependent fumarate hydratase
51	326	Pfam	PF05681	Fumarate hydratase (Fumerase)
51	326	InterPro	IPR004646	Fe-S hydro-lyase, tartrate dehydratase alpha-type, catalytic domain
3	539	PANTHER	PTHR30389	FUMARATE HYDRATASE-RELATED
74	325	NCBIfam	TIGR00722	hydrolyase, tartrate alpha subunit/fumarate domain protein, Fe-S type
74	325	InterPro	IPR004646	Fe-S hydro-lyase, tartrate dehydratase alpha-type, catalytic domain

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 #20

0.412

Likely same site as P2Rank 3 8.0 Å 5 shared residues 42% of smaller site

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Surrounding area

Site 2 FPocket #17

0.284

Likely same site as P2Rank 5 1.6 Å 7 shared residues 100% of smaller site

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Surrounding area

Site 3 FPocket #15

0.202

Likely same site as P2Rank 4 3.7 Å 7 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

0.817

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Surrounding area

Site 2 P2Rank #2

0.077

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Surrounding area

Site 3 P2Rank #3

0.072

Likely same site as FPocket 17 6.0 Å 5 shared residues 50% of smaller site

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Surrounding area

Site 4 P2Rank #4

0.029

Likely same site as FPocket 15 3.7 Å 7 shared residues 100% of smaller site

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Surrounding area

Site 5 P2Rank #5

0.026

Likely same site as FPocket 17 1.6 Å 7 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

0.777

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Surrounding area

Site 2 P2Rank #2

0.087

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Surrounding area

Site 3 P2Rank #3

0.054

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Surrounding area

Site 4 P2Rank #4

0.04

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Surrounding area

Site 5 P2Rank #5

0.025

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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_A0A0H3GP67	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05015	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.

47 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 6 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 41 similarity-based ZINC candidates

Best available ligand signal

F3S PDB via homolog 295.8 Da · LogP 2.59 · TPSA 0.0 Open detail RCSB PDB

FUM PDB via homolog Detail RCSB PDB

JYD PDB via homolog Detail RCSB PDB

LMR PDB via homolog Detail RCSB PDB

MLA 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
F3S RCSB PDB	6UOI	E9AE57	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
FUM RCSB PDB	6UQN	E9AE57	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)\C(=O)O`
JYD RCSB PDB	6MSN	E9AE57	150.2 Da LogP -0.16 TPSA 74.6	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)S)C(=O)O`
LMR RCSB PDB	5L2R	E9AE57	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)O)C(=O)O`
MLA RCSB PDB	5L2R	E9AE57	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
SIN RCSB PDB	6UOJ	E9AE57	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=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
ZINC71773889 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC1529497 ZINC	0.615	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045 ZINC	0.615	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115 ZINC	0.615	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020 ZINC	0.615	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440 ZINC	0.615	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	0.615	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062 ZINC	0.615	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC1572706 ZINC	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC1728397 ZINC	0.533	233.2 Da LogP -0.29 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCC(=O)O`
ZINC2517013 ZINC	0.533	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC1697439 ZINC	0.529	219.5 Da LogP 1.79 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(Cl)(Cl)Cl`
ZINC35465466 ZINC	0.529	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC39208104 ZINC	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=O)O`
ZINC100473925 ZINC	0.500	256.2 Da LogP -1.50 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)/C=C\C(=O)NCCNC(=O)/C=C\C(=O)O`
ZINC138079998 ZINC	0.500	212.0 Da LogP 1.41 TPSA 37.3	✓ Ro5	✓ Clean	`C=C(I)CC(=O)O`
ZINC145743383 ZINC	0.500	266.2 Da LogP 0.77 TPSA 129.0	✓ Ro5	✓ Clean	`O=C(O)CCP(=O)(CCC(=O)O)CCC(=O)O`
ZINC1542984448 ZINC	0.500	470.5 Da LogP 0.07 TPSA 148.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC1577651 ZINC	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652 ZINC	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653 ZINC	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC1586444 ZINC	0.500	210.2 Da LogP -0.65 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)CCS(=O)(=O)CCC(=O)O`
ZINC1679042 ZINC	0.500	256.2 Da LogP -1.50 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)/C=C/C(=O)NCCNC(=O)/C=C/C(=O)O`
ZINC1753095 ZINC	0.500	238.3 Da LogP 1.40 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCSCCSCCC(=O)O`
ZINC22028383 ZINC	0.500	204.2 Da LogP -0.88 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(O)CCNCCNCCC(=O)O`
ZINC22576322 ZINC	0.500	348.4 Da LogP -0.51 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCN(CCC(=O)O)CCC(=O)O`
ZINC26897400 ZINC	0.500	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813 ZINC	0.500	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725 ZINC	0.500	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC35977596 ZINC	0.500	294.3 Da LogP 0.00 TPSA 111.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCC(=O)O`
ZINC38682833 ZINC	0.500	286.3 Da LogP -0.61 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N1CCN(C(=O)CCC(=O)O)CC1`
ZINC39383060 ZINC	0.500	206.2 Da LogP -0.03 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCC(=O)O`
ZINC39427081 ZINC	0.500	250.2 Da LogP -0.01 TPSA 102.3	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCC(=O)O`
ZINC4822898 ZINC	0.500	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900 ZINC	0.500	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC4866352 ZINC	0.500	282.3 Da LogP -1.06 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)/C=C/C(=O)N1CCN(C(=O)/C=C/C(=O)O)CC1`
ZINC71257127 ZINC	0.500	426.5 Da LogP 0.05 TPSA 139.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC71257128 ZINC	0.500	338.4 Da LogP 0.02 TPSA 120.8	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCC(=O)O`
ZINC79016464 ZINC	0.500	382.4 Da LogP 0.04 TPSA 130.0	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC8616656 ZINC	0.500	256.2 Da LogP -1.50 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)C=CC(=O)NCCNC(=O)C=CC(=O)O`
ZINC90623560 ZINC	0.500	256.2 Da LogP -1.50 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)/C=C\C(=O)NCCNC(=O)/C=C/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.