KpATCC43816 Protein target profile

mannose-6-phosphate isomerase, class I

Accession: VK055_0991

Gene: AIK79614.1 manA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GS87
Length 392
Pocket druggability (P2Rank · AlphaFold DB model) 0.834
Metabolic reactions 3
Chokepoint Yes
Direct ligand evidence 0 52 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 (%)
39.791 Lower values reduce human off-target concern.
Human E-value
1.47e-29
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
97.85 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) 0.834
Structure A0A0H3GS87
Pocket Pocket 1
Druggability (FPocket) 0.226
Structure A0A0H3GS87
Pocket Pocket 9
ColabFold model
P2Rank 0.801 · Pocket 1
FPocket 0.281 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Amino sugar and nucleotide sugar metabolism.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

3 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MQKLINAVQNYAWGSHTALTELYGIANPDNLPMAELWMGAHPKSSSQILAADGQPRSLREVIDADKAALLGDKVAARFGELPFLFKVLCAAQPLSIQVHPNKQASEEGFARENAAGIPLSAAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVTLLQPVASAHPAIGAFLQQPDATHLSQLFASLLNMQGEEKAKALQVLRDVLAREQGEPWQTIRLIAEFYPDDSGLFSPLLLNVVKLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPAGELLTQPQRHGAELDFPIPVEDFAFSLHDLSAEASDLAQASAAIVFCVDGEAVLRKGDQSLTLKPGESAFVAASESPVQVSGRGRVARVFNKLQ

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:0008270 Binding to a zinc ion (Zn).
  • GO:0009298 The chemical reactions and pathways resulting in the formation of GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
  • GO:0004476 Catalysis of the reaction: D-mannose 6-phosphate = D-fructose 6-phosphate.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
301 382 Gene3D G3DSA:2.60.120.10 Jelly Rolls
301 382 InterPro IPR014710 RmlC-like jelly roll fold
2 380 PANTHER PTHR10309 MANNOSE-6-PHOSPHATE ISOMERASE
2 380 InterPro IPR016305 Mannose-6-phosphate isomerase
4 382 NCBIfam TIGR00218 mannose-6-phosphate isomerase, class I
4 382 InterPro IPR001250 Mannose-6-phosphate isomerase, type I
1 375 SUPERFAMILY SSF51182 RmlC-like cupins
1 375 InterPro IPR011051 RmlC-like cupin domain superfamily
1 150 Pfam PF20511 Phosphomannose isomerase type I, catalytic domain
1 150 InterPro IPR046457 Phosphomannose isomerase type I, catalytic domain
4 293 CDD cd07011 cupin_PMI_type_I_N
1 392 PIRSF PIRSF001480 PMI
1 392 InterPro IPR016305 Mannose-6-phosphate isomerase
81 102 PRINTS PR00714 Phosphomannose isomerase type I signature
81 102 InterPro IPR016305 Mannose-6-phosphate isomerase
255 274 PRINTS PR00714 Phosphomannose isomerase type I signature
255 274 InterPro IPR016305 Mannose-6-phosphate isomerase
274 293 PRINTS PR00714 Phosphomannose isomerase type I signature
274 293 InterPro IPR016305 Mannose-6-phosphate isomerase
126 149 PRINTS PR00714 Phosphomannose isomerase type I signature
126 149 InterPro IPR016305 Mannose-6-phosphate isomerase
220 235 PRINTS PR00714 Phosphomannose isomerase type I signature
220 235 InterPro IPR016305 Mannose-6-phosphate isomerase
236 255 PRINTS PR00714 Phosphomannose isomerase type I signature
236 255 InterPro IPR016305 Mannose-6-phosphate isomerase
32 47 PRINTS PR00714 Phosphomannose isomerase type I signature
32 47 InterPro IPR016305 Mannose-6-phosphate isomerase
4 22 PRINTS PR00714 Phosphomannose isomerase type I signature
4 22 InterPro IPR016305 Mannose-6-phosphate isomerase
150 300 Gene3D G3DSA:1.10.441.10 Phosphomannose Isomerase, domain 2
6 275 Gene3D G3DSA:2.60.120.10 Jelly Rolls
6 275 InterPro IPR014710 RmlC-like jelly roll fold
5 174 FunFam G3DSA:2.60.120.10:FF:000030 Mannose-6-phosphate isomerase ManA
255 280 ProSitePatterns PS00966 Phosphomannose isomerase type I signature 2.
255 280 InterPro IPR018050 Phosphomannose isomerase, type I, conserved site
157 236 Pfam PF20512 Phosphomannose isomerase type I, helical insertion domain
157 236 InterPro IPR046458 Phosphomannose isomerase type I, helical insertion domain
310 357 Pfam PF01238 Phosphomannose isomerase type I C-terminal
310 357 InterPro IPR046456 Phosphomannose isomerase type I, C-terminal domain
126 134 ProSitePatterns PS00965 Phosphomannose isomerase type I signature 1.
126 134 InterPro IPR018050 Phosphomannose isomerase, type I, conserved site

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.834
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.072
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.06
Likely same site as FPocket 9 1.2 Å 6 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.032
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.022
Likely same site as FPocket 9 8.0 Å 2 shared residues 22% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #9
0.226
Likely same site as P2Rank 3 1.2 Å 6 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:274-274
UniProt: Binding site:134-134
UniProt: Binding site:255-255
UniProt: Binding site:97-97
UniProt: Binding site:99-99
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_A0A0H3GS87
AlphaFold DB full sequence Viewing
ColabFold VK055_0991
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
9C2 PDB via homolog 260.1 Da · LogP -3.83 · TPSA 182.6 Open detail RCSB PDB
Y1 PDB via homolog Detail RCSB PDB
ZINC12502210 ZINC proposed compound · Tanimoto 0.647 Detail ZINC
ZINC12502212 ZINC proposed compound · Tanimoto 0.647 Detail ZINC
ZINC12502214 ZINC proposed compound · Tanimoto 0.647 Detail ZINC

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
9C2 RCSB PDB P34948 260.1 Da LogP -3.83 TPSA 182.6 1 viol. ✓ Clean C([C@H]([C@H]([C@@H](C(=O)NN)O)O)O)OP(=O)(O)O
Y1 RCSB PDB P25081 88.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Y+2]

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.