Protein profile

KP13_04990

Glutamate dehydrogenase

Genome: KpKP13

Gene: AHE44837.1 Structure source: AlphaFold + ColabFold UniProt A0A060VIF0
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Amino acids 424
Annotations 7
Features 30
PDB binders 6
Druggability 0.151

Overview

Basic information about this protein and its source genome.

Accession
KP13_04990
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44837.1
Status
annotated
Amino acids
424
Structure source
AlphaFold + ColabFold
GO
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. GO:0016639 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP. GO:0004352 Catalysis of the reaction: L-glutamate + NAD+ + H2O = 2-oxoglutarate + NH4+ + NADH + H+. GO:0004354 Catalysis of the reaction: L-glutamate + NADP+ + H2O = 2-oxoglutarate + NH4+ + NADPH + H+. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
49.333
Human E-value
2.32e-20
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
64.678
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.9

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 0.151
Structure A0A060VIF0
Pocket Pocket 23
P2Rank 0.956
Structure A0A060VIF0
Pocket Pocket 1
ColabFold model
FPocket 0.14 · Pocket 22
P2Rank 0.948 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 84 / 4744 genomes with a hit
Normalized 0.018

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0016639 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0004352 Catalysis of the reaction: L-glutamate + NAD+ + H2O = 2-oxoglutarate + NH4+ + NADH + H+.
  • GO:0004354 Catalysis of the reaction: L-glutamate + NADP+ + H2O = 2-oxoglutarate + NH4+ + NADPH + H+.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0006538 The chemical reactions and pathways resulting in the breakdown of L-glutamate.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
9 423 PIRSF PIRSF000185 Glu_DH
9 423 InterPro IPR014362 Glutamate dehydrogenase
10 190 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
10 190 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
188 420 Pfam PF00208 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
188 420 InterPro IPR006096 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
188 423 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
188 423 InterPro IPR036291 NAD(P)-binding domain superfamily
221 241 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
221 241 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
179 201 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
179 201 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
99 113 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
99 113 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
348 359 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
348 359 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
44 187 FunFam G3DSA:3.40.50.10860:FF:000003 Glutamate dehydrogenase
195 349 Gene3D G3DSA:3.40.50.720 -
107 120 ProSitePatterns PS00074 Glu / Leu / Phe / Val dehydrogenases active site.
107 120 InterPro IPR033524 Leu/Phe/Val dehydrogenases active site
42 170 Pfam PF02812 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
42 170 InterPro IPR006097 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain
376 423 Gene3D G3DSA:1.10.8.1210 -
190 420 SMART SM00839 ELFV_dehydrog_3
190 420 InterPro IPR006096 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
12 415 PANTHER PTHR11606 GLUTAMATE DEHYDROGENASE
188 412 CDD cd01076 NAD_bind_1_Glu_DH
188 412 InterPro IPR033922 NAD(P) binding domain of glutamate dehydrogenase
40 175 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase, chain A, domain 1
3 350 Gene3D G3DSA:1.10.8.1210 -

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 + 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_A0A060VIF0
AlphaFold — — full sequence — Viewing
ColabFold KP13_04990
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 26.28 0.912
2 1.99 0.042

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.

58 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
AKG
1HWY
P00366 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
B1T
3ETD
P00366 356.1 Da LogP 5.86 TPSA 40.5 1 viol. ✓ Clean c1c(cc(c(c1Sc2cc(cc(c2O)Cl)Cl)O)Cl)Cl
GWD
3ETG
P00366 520.9 Da LogP 5.01 TPSA 49.3 2 viol. ✓ Clean c1cc2c(cc1I)/C(=C\c3cc(c(c(c3)Br)O)Br)/C(=O)N2
H3P
3ETE
P00366 406.9 Da LogP 6.61 TPSA 40.5 1 viol. ✓ Clean c1c(c(c(c(c1Cl)Cl)Cc2c(c(cc(c2Cl)Cl)Cl)O)O)Cl
NH4
3AOG
Q72IC1 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
XEG
6DHL
P00366 442.4 Da LogP 2.53 TPSA 177.1 1 viol. Alert c1cc(c(cc1[C@@H]2[C@H](Cc3c(cc(cc3O2)O)O)OC(=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.