Protein profile

KP13_05411

NADP-specific glutamate dehydrogenase

Genome: KpKP13

Gene: AHE45055.1 gdhA Structure source: AlphaFold + ColabFold UniProt A0A0H3GN61
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Amino acids 447
Annotations 7
Features 32
PDB binders 7
Druggability 0.361

Overview

Basic information about this protein and its source genome.

Accession
KP13_05411
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45055.1 gdhA
Status
annotated
Amino acids
447
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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 (%)
31.771
Human E-value
4.71e-17
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
55.251
DEG E-value
0.0
Localization
Unknown
ColabFold pLDDT
96.44

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 0.361
Structure A0A0H3GN61
Pocket Pocket 14
P2Rank 0.889
Structure A0A0H3GN61
Pocket Pocket 1
ColabFold model
FPocket 0.285 · Pocket 24
P2Rank 0.846 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3218 / 4744 genomes with a hit
Normalized 0.678

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
22 447 PIRSF PIRSF000185 Glu_DH
22 447 InterPro IPR014362 Glutamate dehydrogenase
7 196 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
7 196 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
195 446 CDD cd05313 NAD_bind_2_Glu_DH
195 446 InterPro IPR033922 NAD(P) binding domain of glutamate dehydrogenase
383 447 Gene3D G3DSA:1.10.285.10 Glutamate Dehydrogenase, chain A, domain 3
6 446 PANTHER PTHR43571 NADP-SPECIFIC GLUTAMATE DEHYDROGENASE 1-RELATED
209 374 FunFam G3DSA:3.40.50.720:FF:000030 Glutamate dehydrogenase
204 445 SMART SM00839 ELFV_dehydrog_3
204 445 InterPro IPR006096 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
57 184 Pfam PF02812 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
57 184 InterPro IPR006097 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain
55 190 FunFam G3DSA:3.40.50.10860:FF:000002 Glutamate dehydrogenase
122 135 ProSitePatterns PS00074 Glu / Leu / Phe / Val dehydrogenases active site.
122 135 InterPro IPR033524 Leu/Phe/Val dehydrogenases active site
55 190 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase, chain A, domain 1
10 382 Gene3D G3DSA:1.10.285.10 Glutamate Dehydrogenase, chain A, domain 3
379 447 FunFam G3DSA:1.10.285.10:FF:000001 Glutamate dehydrogenase
202 445 Pfam PF00208 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
202 445 InterPro IPR006096 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
202 446 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
202 446 InterPro IPR036291 NAD(P)-binding domain superfamily
209 373 Gene3D G3DSA:3.40.50.720 -
235 255 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
235 255 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
114 128 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
114 128 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
372 383 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
372 383 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
193 215 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
193 215 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase

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

Loading 3D structure...

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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_A0A0H3GN61
AlphaFold — — full sequence — Viewing
ColabFold KP13_05411
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
14 0.361
22 0.33

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 13.15 0.676
2 5.45 0.259

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.

57 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
8G0
5XW0
B6V7E4 166.1 Da LogP 1.08 TPSA 74.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)C(=O)O
A2R
7ECR
T2D1F5 639.3 Da LogP -3.17 TPSA 338.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AKG
5XVV
B6V7E4 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
MLI
7ECS
T2D1F5 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
NH4
3AOG
Q72IC1 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
SIN
7ECR
T2D1F5 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TLA
7ECT
T2D1F5 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.