Protein profile

KP13_05015

Fumarate hydratase class I, aerobic

Genome: KpKP13

Gene: AHE44810.1 fumA Structure source: AlphaFold + ColabFold UniProt A0A0H3GP67
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Amino acids 548
Annotations 9
Features 16
PDB binders 6
Druggability 0.412

Overview

Basic information about this protein and its source genome.

Accession
KP13_05015
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44810.1 fumA
Status
annotated
Amino acids
548
Structure source
AlphaFold + ColabFold
EC
4.2.1.2
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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.34

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 0.412
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
Normalized 0.154

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GP67
AlphaFold — — full sequence — Viewing
ColabFold KP13_05015
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
20 0.412
17 0.284
15 0.202

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 Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 11.72 0.623
2 2.68 0.079
3 1.33 0.015

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

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
F3S
6UOI
E9AE57 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
FUM
6UQN
E9AE57 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
JYD
6MSN
E9AE57 150.2 Da LogP -0.16 TPSA 74.6 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)S)C(=O)O
LMR
5L2R
E9AE57 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MLA
5L2R
E9AE57 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
SIN
6UOJ
E9AE57 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=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.