KpKP13 Protein target profile

D,D-heptose 1,7-bisphosphate phosphatase

Accession: KP13_01778

Gene: AHE46218.1 gmhB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIP4

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Length 188

Pocket druggability (P2Rank · AlphaFold DB model) 0.345

Direct ligand evidence 0 21 total records

Functional annotation 1 EC 6 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. Moderate predicted binding pocket FPocket selected-pocket score 0.45. This supports review but is not experimental 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: 3.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 62.766 Higher values support similarity to known essential genes.
DEG E-value: 8.06e-83 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 97.13 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) 0.345

Structure A0A0H3GIP4

Pocket Pocket 1

Druggability (FPocket) 0.448

Structure A0A0H3GIP4

Pocket Pocket 3

ColabFold model

P2Rank 0.39 · Pocket 1

FPocket 0.393 · Pocket 3

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 173 / 4744 genomes with a hit

Prevalence 3.6%

Sequence

Primary amino-acid sequence viewer.

MAKSVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKEMGYALVLVTNQSGIARGKFTEAQFETLTEWMDWSLADRGVDLDGIYYCPHHPQGAVEEYRQTCDCRKPHPGMLISARDYLHIDMAASYMVGDKLEDMQAAAAADVGTKVLVRTGKPLTEEAEKAADWVLNSLAELPAAIKKQQK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

3.1.3.-

Gene Ontology (GO)

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:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0034200 Catalysis of the reaction: D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-beta-D-manno-heptose 1-phosphate + phosphate.
GO:0046872 Binding to a metal ion.
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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
3	187	SFLD	SFLDG01134	C1.5.5: Heptose Bisphosphate Phosphatase Like
6	151	CDD	cd07503	HAD_HisB-N
1	188	PIRSF	PIRSF004682	GmhB
1	188	InterPro	IPR004446	D,D-heptose 1,7-bisphosphate phosphatase
4	188	Gene3D	G3DSA:3.40.50.1000	-
4	188	InterPro	IPR023214	HAD superfamily
7	151	NCBIfam	TIGR01662	HAD-IIIA family hydrolase
7	151	InterPro	IPR006549	HAD-superfamily hydrolase,subfamily IIIA
6	153	NCBIfam	TIGR01656	histidinol-phosphate phosphatase domain
6	153	InterPro	IPR006543	Histidinol-phosphate phosphatase
6	180	NCBIfam	TIGR00213	D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase
6	180	InterPro	IPR004446	D,D-heptose 1,7-bisphosphate phosphatase
109	179	Pfam	PF13242	HAD-hyrolase-like
3	186	PANTHER	PTHR42891	D-GLYCERO-BETA-D-MANNO-HEPTOSE-1,7-BISPHOSPHATE 7-PHOSPHATASE
3	186	InterPro	IPR004446	D,D-heptose 1,7-bisphosphate phosphatase
2	185	SUPERFAMILY	SSF56784	HAD-like
2	185	InterPro	IPR036412	HAD-like superfamily
3	187	SFLD	SFLDS00003	Haloacid Dehalogenase
4	187	FunFam	G3DSA:3.40.50.1000:FF:000037	D,D-heptose 1,7-bisphosphate phosphatase

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

0.345

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.033

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3

0.448

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:11-11 Nucleophile

UniProt: Active site:13-13 Proton donor

UniProt: Binding site:107-107

UniProt: Binding site:109-109

UniProt: Binding site:11-11

UniProt: Binding site:11-13

UniProt: Binding site:110-111

UniProt: Binding site:13-13

UniProt: Binding site:136-136

UniProt: Binding site:137-137

UniProt: Binding site:19-22

UniProt: Binding site:53-56

UniProt: Binding site:92-92

UniProt: Binding site:94-94

UniProt: Site:110-110 Contributes to substrate recognition

UniProt: Site:111-111 Stabilizes the phosphoryl group

UniProt: Site:53-53 Stabilizes the phosphoryl group

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_A0A0H3GIP4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01778	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.

21 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 20 similarity-based ZINC candidates

Best available ligand signal

GMB PDB via homolog 370.1 Da · LogP -3.63 · TPSA 223.7 Open detail RCSB PDB

ZINC12502703 ZINC proposed compound · Tanimoto 0.550 Detail ZINC

ZINC4095589 ZINC proposed compound · Tanimoto 0.550 Detail ZINC

ZINC13522068 ZINC proposed compound · Tanimoto 0.525 Detail ZINC

ZINC3870205 ZINC proposed compound · Tanimoto 0.525 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
GMB RCSB PDB	3L8G	P63228	370.1 Da LogP -3.63 TPSA 223.7	1 viol.	✓ Clean	`C([C@@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O…`

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
ZINC12502703 ZINC	0.550	340.1 Da LogP -2.99 TPSA 203.4	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@H](O)[C@…`
ZINC4095589 ZINC	0.550	340.1 Da LogP -2.99 TPSA 203.4	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@…`
ZINC13522068 ZINC	0.525	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@…`
ZINC3870205 ZINC	0.525	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@@H](O)[C…`
ZINC4095560 ZINC	0.525	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@H](O)[C@…`
ZINC1532536 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@@H](CO)[C@H](O)[C@@H](O)[C@…`
ZINC1532537 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@@H](CO)[C@H](O)[C@@H](O)[C…`
ZINC1532880 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@…`
ZINC35976710 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@…`
ZINC3869662 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@@…`
ZINC3869663 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@@H](CO)[C@H](O)[C@H](O)[C@…`
ZINC3869664 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC3869665 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C…`
ZINC3953999 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC4073375 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC4095569 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@…`
ZINC4095578 ZINC	0.500	274.1 Da LogP -3.01 TPSA 174.0	1 viol.	✓ Clean	`O=C(O)[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H](O)…`
ZINC4096091 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H…`
ZINC4096092 ZINC	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]…`
ZINC4096292 ZINC	0.500	274.1 Da LogP -3.01 TPSA 174.0	1 viol.	✓ Clean	`O=C(O)[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H](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 A0A0H3GIP4