KpKP13 Protein target profile

Phosphoheptose isomerase

Accession: KP13_31633

Gene: AHE46203.1 gmhA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIQ6

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Length 193

Pocket druggability (P2Rank · AlphaFold DB model) 0.061

Direct ligand evidence 0 51 total records

Functional annotation 1 EC 7 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.82. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: 6.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 92.708 Higher values support similarity to known essential genes.
DEG E-value: 6.19e-134 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 97.71 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) 0.061

Structure A0A0H3GIQ6

Pocket Pocket 1

Druggability (FPocket) 0.821

Structure A0A0H3GIQ6

Pocket Pocket 1

ColabFold model

P2Rank 0.083 · Pocket 1

FPocket 0.37 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 319 / 4744 genomes with a hit

Prevalence 6.7%

Sequence

Primary amino-acid sequence viewer.

MYQDLIRNELNEAAETLANFLQDEANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHLSCVSNDFGYEYVFSRYVESVGRAGDVLLGISTSGNSGNVIKAIEAARAQGMKVITLTGKDGGKMAGSADVEIRVPHFGYADRIQEIHIKVIHILIMLIEKEMAKG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

5.3.1.28

Gene Ontology (GO)

GO:1901135 The chemical reactions and pathways involving carbohydrate derivative.
GO:0008968 Catalysis of the reaction: D-sedoheptulose-7-phosphate = D-alpha,beta-D-heptose 7-phosphate.
GO:0097367 Binding to a carbohydrate derivative.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0008270 Binding to a zinc ion (Zn).
GO:2001061 The chemical reactions and pathways resulting in the formation of a D-glycero-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.

15 records

Show feature table

Start	End	DB	Term	Name
37	193	ProSiteProfiles	PS51464	SIS domain profile.
37	193	InterPro	IPR001347	SIS domain
1	192	FunFam	G3DSA:3.40.50.10490:FF:000013	Phosphoheptose isomerase
12	146	Pfam	PF13580	SIS domain
12	146	InterPro	IPR001347	SIS domain
1	192	PANTHER	PTHR30390	SEDOHEPTULOSE 7-PHOSPHATE ISOMERASE / DNAA INITIATOR-ASSOCIATING FACTOR FOR REPLICATION INITIATION
1	189	SUPERFAMILY	SSF53697	SIS domain
1	189	InterPro	IPR046348	SIS domain superfamily
1	190	Hamap	MF_00067	Phosphoheptose isomerase [gmhA].
1	190	InterPro	IPR004515	Phosphoheptose isomerase
1	192	Gene3D	G3DSA:3.40.50.10490	-
35	187	NCBIfam	TIGR00441	D-sedoheptulose 7-phosphate isomerase
35	187	InterPro	IPR004515	Phosphoheptose isomerase
10	188	CDD	cd05006	SIS_GmhA
10	188	InterPro	IPR035461	GmhA/DiaA

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

0.061

Likely same site as FPocket 6 1.3 Å 7 shared residues 100% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.035

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Surrounding area

Pocket 3 P2Rank #3

0.01

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.821

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Surrounding area

Pocket 2 FPocket #6

0.384

Likely same site as P2Rank 1 1.3 Å 7 shared residues 100% of smaller site

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Surrounding area

Pocket 3 FPocket #8

0.344

Likely same site as P2Rank 1 7.1 Å 2 shared residues 40% of smaller site

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Surrounding area

Pocket 4 FPocket #2

0.274

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Surrounding area

Residue sets

UniProt: Binding site:119-121

UniProt: Binding site:124-124

UniProt: Binding site:172-172

UniProt: Binding site:180-180

UniProt: Binding site:52-54

UniProt: Binding site:61-61

UniProt: Binding site:65-65

UniProt: Binding site:93-94

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.083

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Surrounding area

Pocket 2 P2Rank #2

0.02

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Surrounding area

Pocket 3 P2Rank #3

0.008

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Surrounding area

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_A0A0H3GIQ6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_31633	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.

51 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

I22 PDB via homolog 290.2 Da · LogP -3.90 · TPSA 185.0 Open detail RCSB PDB

ZINC5132038 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC100065511 ZINC proposed compound · Tanimoto 0.897 Detail ZINC

ZINC100085043 ZINC proposed compound · Tanimoto 0.897 Detail ZINC

ZINC104869937 ZINC proposed compound · Tanimoto 0.897 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
I22 RCSB PDB	2I22	P63224	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`C([C@H]([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)O)OP(=…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC5132038 ZINC	1.000	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC100065511 ZINC	0.897	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043 ZINC	0.897	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937 ZINC	0.897	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943 ZINC	0.897	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845 ZINC	0.897	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1529626 ZINC	0.767	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567 ZINC	0.767	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851 ZINC	0.767	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708 ZINC	0.767	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC12501558 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2047359 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604 ZINC	0.688	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502210 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259 ZINC	0.667	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC2516111 ZINC	0.645	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704 ZINC	0.645	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3869812 ZINC	0.645	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100033330 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC100067275 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC100889630 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC104861723 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O…`
ZINC12503760 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC12503763 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC19850142 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC2508229 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4545927 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(…`
ZINC4545928 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O…`
ZINC4545929 ZINC	0.588	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O)(O…`
ZINC3870277 ZINC	0.559	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC100036265 ZINC	0.548	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100071552 ZINC	0.548	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO`
ZINC113074329 ZINC	0.548	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC13522679 ZINC	0.548	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC4353160 ZINC	0.548	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC8579422 ZINC	0.548	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4887588 ZINC	0.543	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=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.

Cross-references

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

Sequence

UniProt A0A0H3GIQ6