Protein profile

KP13_01926

Shikimate dehydrogenase

Genome: KpKP13

Gene: AHE46368.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJ74
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Amino acids 287
Annotations 7
Features 19
PDB binders 5
Druggability 0.312

Overview

Basic information about this protein and its source genome.

Accession
KP13_01926
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46368.1
Status
annotated
Amino acids
287
Structure source
AlphaFold + ColabFold
EC
1.1.1.25
GO
GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. GO:0004764 Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+. GO:0019632 The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids. GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
51.418
DEG E-value
3.42e-110
Localization
Cytoplasmic
ColabFold pLDDT
97.02

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 0.312
Structure A0A0H3GJ74
Pocket Pocket 6
P2Rank 0.89
Structure A0A0H3GJ74
Pocket Pocket 1
ColabFold model
FPocket 0.411 · Pocket 15
P2Rank 0.887 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 369 / 4744 genomes with a hit
Normalized 0.078

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:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0004764 Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
  • GO:0019632 The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.
  • GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
  • GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
  • GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
14 96 Pfam PF08501 Shikimate dehydrogenase substrate binding domain
14 96 InterPro IPR013708 Shikimate dehydrogenase substrate binding, N-terminal
108 274 CDD cd01065 NAD_bind_Shikimate_DH
109 258 FunFam G3DSA:3.40.50.720:FF:000086 Quinate/shikimate dehydrogenase
9 287 Hamap MF_00222 Shikimate dehydrogenase (NADP(+)) [aroE].
9 287 InterPro IPR022893 Shikimate dehydrogenase family
257 284 Pfam PF18317 Shikimate 5'-dehydrogenase C-terminal domain
257 284 InterPro IPR041121 SDH, C-terminal
4 108 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
4 108 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
11 284 NCBIfam TIGR00507 shikimate dehydrogenase
11 284 InterPro IPR011342 Shikimate dehydrogenase
13 275 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase, chain A, domain 1
109 286 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
109 286 InterPro IPR036291 NAD(P)-binding domain superfamily
13 120 FunFam G3DSA:3.40.50.10860:FF:000004 Quinate/shikimate dehydrogenase
3 280 PANTHER PTHR21089 SHIKIMATE DEHYDROGENASE
3 280 InterPro IPR022893 Shikimate dehydrogenase family
110 260 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_A0A0H3GJ74
AlphaFold — — full sequence — Viewing
ColabFold KP13_01926
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
6 0.312

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 12.23 0.643
2 3.54 0.13
3 2.21 0.054
4 1.84 0.036

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.

55 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
ATR
2HK9
O67049 507.2 Da LogP -1.63 TPSA 279.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DHK
2O7Q
Q9SQT8 174.2 Da LogP -0.75 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@@H](C=C([C@H]([C@@H]1O)O)O)C(=O)O
QIC
6BMQ
Q9SQT8 192.2 Da LogP -2.32 TPSA 118.2 ✓ Ro5 ✓ Clean C1[C@H](C([C@@H](CC1(C(=O)O)O)O)O)O
SKM
2HK9
O67049 174.2 Da LogP -1.52 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O
TLA
2GPT
Q9SQT8 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.