Protein profile

KP13_03795

dTDP-4-dehydrorhamnose 3,5-epimerase in cps region

Genome: KpKP13

Gene: AHE43667.1 rmlC Structure source: AlphaFold + ColabFold UniProt A0A0H3GSI9
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Amino acids 184
Annotations 5
Features 12
PDB binders 5
Druggability 0.188

Overview

Basic information about this protein and its source genome.

Accession
KP13_03795
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE43667.1 rmlC
Status
annotated
Amino acids
184
Structure source
AlphaFold + ColabFold
EC
5.1.3.13
GO
GO:0008830 Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate. GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 (%)
64.481
DEG E-value
1.24e-82
Localization
Unknown
ColabFold pLDDT
97.83

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 0.188
Structure A0A0H3GSI9
Pocket Pocket 2
P2Rank 0.641
Structure A0A0H3GSI9
Pocket Pocket 1
ColabFold model
FPocket 0.291 · Pocket 6
P2Rank 0.738 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1559 / 4744 genomes with a hit
Normalized 0.329

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008830 Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
  • GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
5 178 Pfam PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase
5 178 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
2 180 NCBIfam TIGR01221 dTDP-4-dehydrorhamnose 3,5-epimerase
2 180 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
2 178 PANTHER PTHR21047 DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE
2 178 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
1 184 Gene3D G3DSA:2.60.120.10 Jelly Rolls
1 184 InterPro IPR014710 RmlC-like jelly roll fold
3 174 CDD cd00438 cupin_RmlC
3 174 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
1 181 SUPERFAMILY SSF51182 RmlC-like cupins
1 181 InterPro IPR011051 RmlC-like cupin domain superfamily

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_A0A0H3GSI9
AlphaFold — — full sequence — Viewing
ColabFold KP13_03795
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 9.65 0.519
2 0.8 0.003

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.

60 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
ATY
1DZT
P26394 444.2 Da LogP -0.71 TPSA 203.7 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…
SRT
1RTV
Q9HU21 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O
TDO
6NDR
Q5ZXH5 546.3 Da LogP -2.22 TPSA 253.4 3 viol. ✓ Clean C[C@H]1C(=O)[C@H]([C@H]([C@H](O1)O[P@@](=O)(O)O…
TPE
1DZT
P26394 520.3 Da LogP 1.38 TPSA 192.7 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…
TYD
1EPZ
O27818 402.2 Da LogP -1.28 TPSA 197.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.