KpKP13 Protein target profile

ADP-L-glycero-D-manno-heptose-6-epimerase

Accession: KP13_00202

Gene: hldD AHE42116.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUR3
Length 310
Pocket druggability (P2Rank · AlphaFold DB model) 0.988
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 5 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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
Hit
Human identity (%)
25.41 Lower values reduce human off-target concern.
Human E-value
4.21e-06
Gut microbiome similarity
7.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.419 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.35 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.988
Structure A0A0H3GUR3
Pocket Pocket 1
Druggability (FPocket) 0.416
Structure A0A0H3GUR3
Pocket Pocket 1
ColabFold model
P2Rank 0.986 · Pocket 1
FPocket 0.655 · Pocket 13
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 347 / 4744 genomes with a hit
Prevalence 7.3%

Sequence

Primary amino-acid sequence viewer.

MIIVTGGAGFIGSNIVKALNDKGITDILVVDNLKDGTKFVNLVDLNIADYMDKEDFLIQIMAGEEFGEIEAIFHEGACSSTTEWDGKYMMDNNYQYSKELLHYCLEREIPFLYASSAATYGGRTSDFIESREYEQPLNVYGYSKFLFDEYVRQILPEANSQIVGFRYFNVYGPREGHKGSMASVAFHLNTQLNNGESPKLFEGSDGFKRDFVYVGDVADVNLWFWENGVSGIFNLGTGRAESFQAVADATLAYHKKGSIEYIPFPDKLKGRYQAFTQADLTNLRKAGYDKPFKTVAEGVTEYMAWLNRDA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0008712 Catalysis of the reaction: ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose.
  • 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:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0097171 The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
  • GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 308 CDD cd05248 ADP_GME_SDR_e
1 308 InterPro IPR011912 ADP-L-glycero-D-manno-heptose-6-epimerase
168 289 Gene3D G3DSA:3.90.25.10 -
3 302 Gene3D G3DSA:3.40.50.720 -
2 236 Pfam PF01370 NAD dependent epimerase/dehydratase family
2 236 InterPro IPR001509 NAD-dependent epimerase/dehydratase
2 308 NCBIfam TIGR02197 ADP-glyceromanno-heptose 6-epimerase
2 308 InterPro IPR011912 ADP-L-glycero-D-manno-heptose-6-epimerase
1 306 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 306 InterPro IPR036291 NAD(P)-binding domain superfamily
2 308 PANTHER PTHR43103 NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE
1 309 Hamap MF_01601 ADP-L-glycero-D-manno-heptose-6-epimerase [hldD].
1 309 InterPro IPR011912 ADP-L-glycero-D-manno-heptose-6-epimerase

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.988
Likely same site as FPocket 1 0.9 Å 55 shared residues 96% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.103
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.048
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.416 Unusual size
Likely same site as P2Rank 1 0.9 Å 55 shared residues 96% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:140-140 Proton acceptor
UniProt: Active site:178-178 Proton acceptor
UniProt: Binding site:10-11
UniProt: Binding site:144-144
UniProt: Binding site:169-169
UniProt: Binding site:170-170
UniProt: Binding site:178-178
UniProt: Binding site:180-180
UniProt: Binding site:187-187
UniProt: Binding site:201-204
UniProt: Binding site:209-209
UniProt: Binding site:272-272
UniProt: Binding site:31-32
UniProt: Binding site:38-38
UniProt: Binding site:53-53
UniProt: Binding site:75-79
UniProt: Binding site:92-92
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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
AlphaFold DB AF_A0A0H3GUR3
AlphaFold DB full sequence Viewing
ColabFold KP13_00202
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ADQ PDB via homolog 589.3 Da · LogP -3.92 · TPSA 311.7 Open detail RCSB PDB
EPZ PDB via homolog Detail RCSB PDB
GDU PDB via homolog Detail RCSB PDB
UD1 PDB via homolog Detail RCSB PDB
UD2 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
ADQ RCSB PDB P67910 589.3 Da LogP -3.92 TPSA 311.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
EPZ RCSB PDB D3E402 679.4 Da LogP -4.15 TPSA 332.2 3 viol. ✓ Clean C[C@H](C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]…
GDU RCSB PDB A3MUJ4 566.3 Da LogP -4.79 TPSA 297.0 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
UD1 RCSB PDB E5KJ94 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
UD2 RCSB PDB Q4KCF6 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](…
UPG RCSB PDB Q9WYX9 566.3 Da LogP -4.79 TPSA 297.0 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.

Cross-references

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