Protein profile

KP13_00564

5,10-methylenetetrahydrofolate reductase

Genome: KpKP13

Gene: AHE47039.1 metF Structure source: AlphaFold + ColabFold UniProt A0A0H3GGD2
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Amino acids 295
Annotations 8
Features 11
PDB binders 2
Druggability 0.142

Overview

Basic information about this protein and its source genome.

Accession
KP13_00564
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE47039.1 metF
Status
annotated
Amino acids
295
Structure source
AlphaFold + ColabFold
EC
1.5.1.54
GO
GO:0006555 The chemical reactions and pathways involving L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. GO:0004489 Catalysis of the reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + H+. GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0106312 Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + NAD+ = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADH + H+.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
38.22
Human E-value
3.5199999999999996e-24
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
41.667
DEG E-value
4.1800000000000005e-73
Localization
Cytoplasmic
ColabFold pLDDT
95.98

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 0.142
Structure A0A0H3GGD2
Pocket Pocket 21
P2Rank 0.906
Structure A0A0H3GGD2
Pocket Pocket 1
ColabFold model
FPocket 0.43 · Pocket 1
P2Rank 0.935 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0006555 The chemical reactions and pathways involving L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
  • GO:0004489 Catalysis of the reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + H+.
  • GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0106312 Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + NAD+ = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADH + H+.
  • GO:0035999 The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
1 295 FunFam G3DSA:3.20.20.220:FF:000001 Methylenetetrahydrofolate reductase
22 294 SUPERFAMILY SSF51730 FAD-linked oxidoreductase
22 294 InterPro IPR029041 FAD-linked oxidoreductase-like
19 292 PANTHER PTHR45754 METHYLENETETRAHYDROFOLATE REDUCTASE
25 290 NCBIfam TIGR00676 methylenetetrahydrofolate reductase [NAD(P)H]
25 290 InterPro IPR004620 5,10-methylenetetrahydrofolate reductase
1 295 Gene3D G3DSA:3.20.20.220 -
16 291 Pfam PF02219 Methylenetetrahydrofolate reductase
16 291 InterPro IPR003171 Methylenetetrahydrofolate reductase-like
25 290 CDD cd00537 MTHFR
25 290 InterPro IPR003171 Methylenetetrahydrofolate reductase-like

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_A0A0H3GGD2
AlphaFold — — full sequence — Viewing
ColabFold KP13_00564
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 20.53 0.857

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.

52 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
4HF
2FMN
P0AEZ1 449.5 Da LogP 0.68 TPSA 187.5 1 viol. ✓ Clean c1cc(sc1CC[C@@H]2CC3=C(NC2)N=C(NC3=O)N)C(=O)N[C…
C2F
1ZP4
P0AEZ1 459.5 Da LogP -0.26 TPSA 202.8 1 viol. ✓ Clean C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…

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.