Protein target profile

KP13_01696

Lipopolysaccharide biosynthesis protein rffA

Genome: KpKP13 Gene: rffA AHE46998.1 3D evidence: Experimental + ColabFold model UniProt A6TGH9
Length 376
Pocket druggability 0.997
Direct ligand evidence 0 58 total records
Functional annotation 0 EC 3 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
9.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.96 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.997
Structure 6BLG
Pocket Pocket 1
P2Rank 0.636
Structure 6BLG
Pocket Pocket 1
ColabFold model
FPocket 0.708 · Pocket 3
P2Rank 0.905 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 455 / 4744 genomes with a hit
Prevalence 9.6%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Structure

Sequence

Primary amino-acid sequence viewer.

MIPFNAPPVVGTELDYMQSAMNSGKLCGDGGFTRRCQQWMEQRFGTAKALLTPSCTASLEMAALLLDIQPGDEVIMPSYTFVSTANAFVLRGAKIVFVDIRRDTMNIDETLIEAAITDKTRAIVPVHYAGVACEMDTIMAIADKYNLFVVEDAAQGVMSTYKGRALGTIGHIGCFSFHETKNYTAGGEGGATLINDRTLVERAEIIREKGTNRSQFFRGLVDKYTWRDIGSSYLMSDLQAAYLWAQLEAAERINQQRLALWQNYYDALLPLARAGRIELPTVPADCGQNAHMFYIKLRDIEDRSRLIAWLKEAEILAVFHYIPLHSCPAGEQFGEFRGEDRYTTQESERLVRLPLFYNLSVVNQRTVINSLLSYFS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0009246 The chemical reactions and pathways resulting in the formation of the enterobacterial common antigen, an acidic polysaccharide containing N-acetyl-D-glucosamine, N-acetyl-D-mannosaminouronic acid, and 4-acetamido-4,6-dideoxy-D-galactose. A major component of the cell wall outer membrane of Gram-negative bacteria.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0019180 Catalysis of the reaction: dTDP-4-amino-4,6-dideoxy-alpha-D-galactose + 2-oxoglutarate = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + L-glutamate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
250 376 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
250 376 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 249 Gene3D G3DSA:3.40.640.10 -
1 249 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 249 FunFam G3DSA:3.40.640.10:FF:000037 dTDP-4-amino-4,6-dideoxygalactose transaminase
1 371 PANTHER PTHR30244 TRANSAMINASE
1 371 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
250 376 FunFam G3DSA:3.90.1150.10:FF:000061 dTDP-4-amino-4,6-dideoxygalactose transaminase
13 371 CDD cd00616 AHBA_syn
13 371 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
13 371 Pfam PF01041 DegT/DnrJ/EryC1/StrS aminotransferase family
2 375 SUPERFAMILY SSF53383 PLP-dependent transferases
2 375 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
1 376 PIRSF PIRSF000390 PLP_StrS
1 376 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
1 376 NCBIfam TIGR02379 dTDP-4-amino-4,6-dideoxy-D-glucose transaminase
1 376 InterPro IPR012749 dTDP-4-amino-4,6-dideoxygalactose transaminase WecE-like
1 376 Hamap MF_02026 dTDP-4-amino-4,6-dideoxygalactose transaminase [wecE].
1 376 InterPro IPR032894 dTDP-4-amino-4,6-dideoxygalactose transaminase WecE

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.997
Likely same site as P2Rank 1 6.9 Å 13 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.636
Likely same site as FPocket 1 6.9 Å 13 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.159
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.016
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6BLG
X-ray A Viewing
ColabFold KP13_01696
ColabFold full sequence Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB
DCS PDB via homolog Detail RCSB PDB
G4M PDB via homolog Detail RCSB PDB
GPD PDB via homolog Detail RCSB PDB
PGU PDB via homolog Detail RCSB PDB

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 RCSB PDB Q8ZNF3 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
DCS RCSB PDB Q8ZNF3 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
G4M RCSB PDB Q9A9H3 819.5 Da LogP -2.79 TPSA 403.2 3 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2[C@H](O[C@@H]…
GPD RCSB PDB Q9A9H3 572.4 Da LogP -2.61 TPSA 297.0 3 viol. ✓ Clean C[C@@H]1[C@H](C[C@@H]([C@H](O1)O[P@](=O)(O)O[P@…
PGU RCSB PDB Q9ZGH4 378.3 Da LogP 0.11 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)C(=O…
PMP RCSB PDB Q8ZNF3 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
T5K RCSB PDB P27833 776.5 Da LogP -1.28 TPSA 348.5 3 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2[C@H](O[C@@…
TQP RCSB PDB Q6TFC4 776.5 Da LogP -1.28 TPSA 348.5 3 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@H]2[C@@H]([C@H…

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.