Protein profile

PA4470

fumarate hydratase

Genome: NC_002516.2

Gene: fumC1 Structure source: ColabFold
Amino acids 458
Annotations 6
Features 32
PDB binders 18
Druggability 0.894

Overview

Basic information about this protein and its source genome.

Accession
PA4470
Gene
fumC1
Status
annotated
Amino acids
458
Structure source
ColabFold
GO
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: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:0004333 Catalysis of the reaction: (S)-malate = fumarate + H2O. 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:0045239 Any of the heteromeric enzymes that act in the TCA cycle. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
44.096
Human E-value
8.58e-112
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.894
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • 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: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:0004333 Catalysis of the reaction: (S)-malate = fumarate + H2O.
  • 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:0045239 Any of the heteromeric enzymes that act in the TCA cycle.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
4 456 Hamap MF_00743 Fumarate hydratase class II [fumC].
4 456 InterPro IPR005677 Fumarate hydratase, class II
3 454 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE
3 454 InterPro IPR005677 Fumarate hydratase, class II
2 132 Gene3D G3DSA:1.10.275.10 -
2 132 InterPro IPR024083 Fumarase/histidase, N-terminal
133 400 FunFam G3DSA:1.20.200.10:FF:000001 Fumarate hydratase, mitochondrial
402 454 Pfam PF10415 Fumarase C C-terminus
402 454 InterPro IPR018951 Fumarase C, C-terminal
127 149 PRINTS PR00145 Argininosuccinate lyase family signature
169 189 PRINTS PR00145 Argininosuccinate lyase family signature
311 327 PRINTS PR00145 Argininosuccinate lyase family signature
401 456 FunFam G3DSA:1.10.40.30:FF:000002 Fumarate hydratase class II
5 132 FunFam G3DSA:1.10.275.10:FF:000001 Fumarate hydratase, mitochondrial
12 336 Pfam PF00206 Lyase
12 336 InterPro IPR022761 Fumarate lyase, N-terminal
174 192 PRINTS PR00149 Fumarate lyase superfamily signature
174 192 InterPro IPR000362 Fumarate lyase family
265 292 PRINTS PR00149 Fumarate lyase superfamily signature
265 292 InterPro IPR000362 Fumarate lyase family
128 146 PRINTS PR00149 Fumarate lyase superfamily signature
128 146 InterPro IPR000362 Fumarate lyase family
311 327 PRINTS PR00149 Fumarate lyase superfamily signature
311 327 InterPro IPR000362 Fumarate lyase family
311 320 ProSitePatterns PS00163 Fumarate lyases signature.
311 320 InterPro IPR020557 Fumarate lyase, conserved site
400 456 Gene3D G3DSA:1.10.40.30 -
3 454 SUPERFAMILY SSF48557 L-aspartase-like
3 454 InterPro IPR008948 L-Aspartase-like
5 453 CDD cd01362 Fumarase_classII
5 453 InterPro IPR005677 Fumarate hydratase, class II
133 399 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain)

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
ColabFold PA4470
ColabFold full sequence Viewing
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
3 0.894
10 0.766
12 0.295

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.

68 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
5WJ P9WN93 470.6 Da LogP 2.68 TPSA 121.5 ✓ Ro5 ✓ Clean COc1ccc(cc1NC(=O)CC2=NNC(=O)c3c2cccc3)S(=O)(=O)…
APO P07954 169.1 Da LogP -1.42 TPSA 120.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)N)P(=O)(O)O
FLC 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 P9WN93 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
KUE P9WN93 484.6 Da LogP 3.07 TPSA 121.5 ✓ Ro5 ✓ Clean COc1ccc(cc1NC(=O)CC2=NNC(=O)c3c2cccc3)S(=O)(=O)…
KYZ P9WN93 402.4 Da LogP 1.02 TPSA 130.2 ✓ Ro5 ✓ Clean CNS(=O)(=O)c1ccc(c(c1)NC(=O)CC2=NNC(=O)c3c2cccc…
KZ8 P9WN93 464.5 Da LogP 2.91 TPSA 130.2 ✓ Ro5 ✓ Clean COc1ccc(cc1NC(=O)CC2=NNC(=O)c3c2cccc3)S(=O)(=O)…
KZK P9WN93 441.6 Da LogP 3.92 TPSA 91.5 ✓ Ro5 ✓ Clean COc1ccc(cc1NC(=O)Cc2c[nH]c3c2cccc3)S(=O)(=O)N4C…
KZN P9WN93 504.6 Da LogP 2.86 TPSA 121.5 1 viol. ✓ Clean COc1ccc(cc1NC(=O)CC2=NNC(=O)c3c2cccc3)S(=O)(=O)…
KZT P9WN93 453.6 Da LogP 3.99 TPSA 88.6 ✓ Ro5 ✓ Clean COc1ccc(cc1NC(=O)Cc2ccnc3c2cccc3)S(=O)(=O)N4CCC…
L0K P9WN93 518.6 Da LogP 2.90 TPSA 121.5 1 viol. ✓ Clean COc1ccc(cc1NC(=O)CC2=NNC(=O)c3c2cccc3)S(=O)(=O)…
LMR B1MKP6 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MLI Q9ZCQ4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MLT P05042 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
PMA 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 P05042 190.3 Da LogP 1.25 TPSA 74.6 ✓ Ro5 ✓ Clean C[Si](C)(C)C(CC(=O)O)C(=O)O
SRT P9WN93 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O
TLA 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.