Protein target profile

VK055_0988

fumarate hydratase, class II

Genome: KpATCC43816 Gene: fumC AIK79612.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GWS1
Length 456
Pocket druggability 0.806
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 9 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.

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 (%)
61.858 Lower values reduce human off-target concern.
Human E-value
2.48e-175
Gut microbiome similarity
19.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
61.674 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.34 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 0.806
Structure A0A0H3GWS1
Pocket Pocket 5
P2Rank 0.124
Structure A0A0H3GWS1
Pocket Pocket 1
ColabFold model
FPocket 0.668 · Pocket 14
P2Rank 0.336 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 939 / 4744 genomes with a hit
Prevalence 19.8%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 99.1% of genes in this genome.

Relative network centrality 99.1% more central than 99.1% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MGAIEVPADKLWGAQTQRSLEHFRISTEKMPGELIYALALTKRAAAKVNQDLGLLTAEKAGAIVAAADEVLAGKHAQEFPLAIWQTGSGTQSNMNMNEVLANRASELLGGERGMARKIHPNDDVNKSQSSNDVFPTAMHVAALIALREKVIPSLQALRATLNEKAVAFRDIVKIGRTHLQDATPLTLGQEISGWVAMLDHSLKHIEASQPHLAELALGGTAVGTGLNTHPEYAVRVAAELASLSGQPFVTAPNKFEALATVDALVHAHGALKGLAASLMKIANDVRWLASGPRCGIGEIAIPENEPGSSIMPGKVNPTQCEALTMVCCQVMGNDVAVNIGGASGNFELNVYRPMVIHNFLQSVRLLADGMASFNEHCAVGIEPNRERISQLLNESLMLVTALNTHIGYDKAAEIAKKAHHEGLTLKASALALGYLTEAEFDSWVRPEEMVGSLAIR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0006106 The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
  • GO:0045239 Any of the heteromeric enzymes that act in the TCA cycle.
  • 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:0004333 Catalysis of the reaction: (S)-malate = fumarate + H2O.
  • 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.
  • 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:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
398 450 Pfam PF10415 Fumarase C C-terminus
398 450 InterPro IPR018951 Fumarase C, C-terminal
398 454 Gene3D G3DSA:1.10.40.30 -
1 451 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE
1 451 InterPro IPR005677 Fumarate hydratase, class II
170 188 PRINTS PR00149 Fumarate lyase superfamily signature
170 188 InterPro IPR000362 Fumarate lyase family
307 323 PRINTS PR00149 Fumarate lyase superfamily signature
307 323 InterPro IPR000362 Fumarate lyase family
261 288 PRINTS PR00149 Fumarate lyase superfamily signature
261 288 InterPro IPR000362 Fumarate lyase family
124 142 PRINTS PR00149 Fumarate lyase superfamily signature
124 142 InterPro IPR000362 Fumarate lyase family
397 454 FunFam G3DSA:1.10.40.30:FF:000002 Fumarate hydratase class II
129 396 FunFam G3DSA:1.20.200.10:FF:000001 Fumarate hydratase, mitochondrial
1 451 NCBIfam TIGR00979 class II fumarate hydratase
1 449 SUPERFAMILY SSF48557 L-aspartase-like
1 449 InterPro IPR008948 L-Aspartase-like
129 397 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain)
1 452 Hamap MF_00743 Fumarate hydratase class II [fumC].
1 452 InterPro IPR005677 Fumarate hydratase, class II
1 128 Gene3D G3DSA:1.10.275.10 -
1 128 InterPro IPR024083 Fumarase/histidase, N-terminal
2 332 Pfam PF00206 Lyase
2 332 InterPro IPR022761 Fumarate lyase, N-terminal
1 449 CDD cd01362 Fumarase_classII
1 449 InterPro IPR005677 Fumarate hydratase, class II
1 128 FunFam G3DSA:1.10.275.10:FF:000001 Fumarate hydratase, mitochondrial
307 316 ProSitePatterns PS00163 Fumarate lyases signature.
307 316 InterPro IPR020557 Fumarate lyase, conserved site

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 #5
0.806
Likely same site as P2Rank 3 5.0 Å 9 shared residues 82% 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
0.124
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Surrounding area
Site 2 P2Rank #2
0.043
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Surrounding area
Site 3 P2Rank #3
0.035
Likely same site as FPocket 5 5.0 Å 9 shared residues 82% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.01
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Surrounding area
Site 5 P2Rank #5
0.006
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Surrounding area
Residue sets
UniProt: Active site:188-188 Proton donor/acceptor
UniProt: Active site:318-318
UniProt: Binding site:129-132 in site B
UniProt: Binding site:139-141
UniProt: Binding site:187-187
UniProt: Binding site:319-319
UniProt: Binding site:324-326
UniProt: Binding site:98-100
UniProt: Site:331-331 Important for catalytic activity
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_A0A0H3GWS1
AlphaFold DB full sequence Viewing
ColabFold VK055_0988
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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
APO PDB via homolog 169.1 Da · LogP -1.42 · TPSA 120.8 Open detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
FUM PDB via homolog Detail RCSB PDB
LMR PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
APO RCSB PDB P07954 169.1 Da LogP -1.42 TPSA 120.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)N)P(=O)(O)O
FLC RCSB PDB P05042 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FUM RCSB PDB Q65UJ3 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
LMR RCSB PDB A0A3Q0KQY7 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MLI RCSB PDB Q9ZCQ4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MLT RCSB PDB P05042 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
PMA RCSB PDB P05042 254.1 Da LogP 0.48 TPSA 149.2 ✓ Ro5 ✓ Clean c1c(c(cc(c1C(=O)O)C(=O)O)C(=O)O)C(=O)O
SIF RCSB PDB P05042 190.3 Da LogP 1.25 TPSA 74.6 ✓ Ro5 ✓ Clean C[Si](C)(C)C(CC(=O)O)C(=O)O
TLA RCSB PDB P07954 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)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.