Protein profile

KP13_00204

L-threonine 3-dehydrogenase

Genome: KpKP13

Gene: tdh AHE42118.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXB7
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Amino acids 341
Annotations 7
Features 20
PDB binders 8
Druggability 0.45

Overview

Basic information about this protein and its source genome.

Accession
KP13_00204
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
tdh AHE42118.1
Status
annotated
Amino acids
341
Structure source
AlphaFold + ColabFold
EC
1.1.1.103
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:0008270 Binding to a zinc ion (Zn). GO:0006567 The chemical reactions and pathways resulting in the breakdown of L-threonine. GO:0008743 Catalysis of the reaction: L-threonine + NAD+ = (2S)-2-amino-3-oxobutanoate + NADH + H+. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0019518 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form 2-amino-3-oxobutanoate, which is subsequently converted to glycine.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.432
Human E-value
1.06e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
97.067
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.7

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 0.45
Structure A0A0H3GXB7
Pocket Pocket 5
P2Rank 0.952
Structure A0A0H3GXB7
Pocket Pocket 1
ColabFold model
FPocket 0.43 · Pocket 11
P2Rank 0.936 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 322 / 4744 genomes with a hit
Normalized 0.068

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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:0008270 Binding to a zinc ion (Zn).
  • GO:0006567 The chemical reactions and pathways resulting in the breakdown of L-threonine.
  • GO:0008743 Catalysis of the reaction: L-threonine + NAD+ = (2S)-2-amino-3-oxobutanoate + NADH + H+.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0019518 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form 2-amino-3-oxobutanoate, which is subsequently converted to glycine.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
20 328 Gene3D G3DSA:3.90.180.10 -
12 338 SMART SM00829 PKS_ER_names_mod
12 338 InterPro IPR020843 Polyketide synthase, enoylreductase domain
153 286 FunFam G3DSA:3.40.50.720:FF:000059 L-threonine 3-dehydrogenase
141 305 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
141 305 InterPro IPR036291 NAD(P)-binding domain superfamily
3 340 NCBIfam TIGR00692 L-threonine 3-dehydrogenase
3 340 InterPro IPR004627 L-threonine 3-dehydrogenase
62 76 ProSitePatterns PS00059 Zinc-containing alcohol dehydrogenases signature.
62 76 InterPro IPR002328 Alcohol dehydrogenase, zinc-type, conserved site
1 173 SUPERFAMILY SSF50129 GroES-like
1 173 InterPro IPR011032 GroES-like superfamily
1 340 Hamap MF_00627 L-threonine 3-dehydrogenase [tdh].
1 340 InterPro IPR004627 L-threonine 3-dehydrogenase
1 340 PANTHER PTHR43401 L-THREONINE 3-DEHYDROGENASE
174 303 Pfam PF00107 Zinc-binding dehydrogenase
174 303 InterPro IPR013149 Alcohol dehydrogenase-like, C-terminal
26 134 Pfam PF08240 Alcohol dehydrogenase GroES-like domain
26 134 InterPro IPR013154 Alcohol dehydrogenase-like, N-terminal
153 286 Gene3D G3DSA:3.40.50.720 -

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_A0A0H3GXB7
AlphaFold — — full sequence — Viewing
ColabFold KP13_00204
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
5 0.45

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 25.36 0.906
2 2.03 0.045

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.

79 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
572
1PL6
Q00796 301.4 Da LogP -1.10 TPSA 89.9 ✓ Ro5 ✓ Clean CN(C)S(=O)(=O)N1CCN(CC1)c2ccnc(n2)CO
BMD
3PII
P42328 87.1 Da LogP 0.27 TPSA 43.1 ✓ Ro5 ✓ Clean CCCC(=O)N
BO3
1E3J
O96496 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
CCB
1U3T
P07327 167.3 Da LogP 1.94 TPSA 20.3 ✓ Ro5 ✓ Clean C1CCC(C1)N(C=O)C2CCC2
ETF
1RJW
P42328 100.0 Da LogP 0.54 TPSA 20.2 ✓ Ro5 ✓ Clean C(C(F)(F)F)O
FU2
3S2F
Q46UZ9 96.1 Da LogP 1.09 TPSA 30.2 ✓ Ro5 ✓ Clean c1cc(oc1)C=O
ISP
3S2F
Q46UZ9 140.1 Da LogP 0.50 TPSA 66.8 ✓ Ro5 ✓ Clean CC(C)OP(=O)(O)O
PYZ
1HSO
P07327 194.0 Da LogP 1.01 TPSA 28.7 ✓ Ro5 ✓ Clean c1c(cn[nH]1)I

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.