Protein target profile

KP13_01100

Translation initiation factor IF-2

Genome: KpKP13 Gene: infB AHE42508.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GY08
Length 896
Pocket druggability 0.644
Direct ligand evidence 0 61 total records
Functional annotation 0 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
41.468 Lower values reduce human off-target concern.
Human E-value
5.97e-126
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
79.13 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.644
Structure A0A0H3GY08
Pocket Pocket 4
P2Rank 0.091
Structure A0A0H3GY08
Pocket Pocket 1
ColabFold model
FPocket 0.463 · Pocket 46
P2Rank 0.244 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Prevalence 3.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTDVTIKALASEIQTSVDRLIQQFADAGIRKSADDSVTSQEKQTLLTHLNREHGSAPDKLTLQRKTRSTLNIPGTGGKSKSVQIEVRKKRTFVKRDPQEAERLAAEEQAQREAEEQARREAEEAAKREAQLKAEREAAEQAKREVADKAKREAAEKDKVSNQHTDEMTKTAQAEKIRRENEAAELKRKSEEEARRKLEEEARRVAEEARRMAEENEKNWSETSDSPEDSSDYHVTTSQHARQAEDDNDREVEGGRGRSRSSKAARPAKKGNKHAESKADREEARAAVRGGKGGKHRKGSALQQGFQKPAQAVNRDVVIGETITVGELANKMAVKGSQVIKAMMKLGAMATINQVIDQETAQLVAEEMGHKVILRRENELEEAVMSDRDTGAAAEPRAPVVTIMGHVDHGKTSLLDYIRSTKVASGEAGGITQHIGAYHVETDNGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDDLLDAILLQAEVLELKAVRNGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRDELGREVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYRQGKFREVKLARQQKSKLENMFANMTEGEVHEVNIVLKADVQGSVEAISDSLLKLSTDEVKVKIIGSGVGGITETDATLAAASNAILVGFNVRADASARKVIEAESLDLRYYSVIYNLIDEVKAAMSGMLSPELKQQIIGLAEVRDVFKSPKFGAIAGCMVTEGTIKRHNPIRVLRDNVVIYEGELESLRRFKDDVNEVRNGMECGIGVKNYNDVRVGDMIEVFEIIEIQRSID

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
  • GO:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0003743 Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
  • GO:0006413 The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0097216 Binding to guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
93 304 MobiDBLite mobidb-lite consensus disorder prediction
802 885 CDD cd03692 mtIF2_IVc
312 895 NCBIfam TIGR00487 translation initiation factor IF-2
312 895 InterPro IPR000178 Translation initiation factor IF-2, bacterial-like
400 556 Pfam PF00009 Elongation factor Tu GTP binding domain
400 556 InterPro IPR000795 Translational (tr)-type GTP-binding domain
238 259 MobiDBLite mobidb-lite consensus disorder prediction
2 50 FunFam G3DSA:3.30.56.50:FF:000001 Translation initiation factor IF-2
393 566 Gene3D G3DSA:3.40.50.300 -
393 566 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 50 Gene3D G3DSA:3.30.56.50 -
57 95 Pfam PF08364 Bacterial translation initiation factor IF-2 associated region
57 95 InterPro IPR013575 Initiation factor 2 associated domain, bacterial
671 785 Pfam PF11987 Translation-initiation factor 2
671 785 InterPro IPR023115 Translation initiation factor IF- 2, domain 3
100 155 Coils Coil Coil
268 289 MobiDBLite mobidb-lite consensus disorder prediction
690 796 FunFam G3DSA:3.40.50.10050:FF:000001 Translation initiation factor IF-2
398 561 CDD cd01887 IF2_eIF5B
567 685 FunFam G3DSA:2.40.30.10:FF:000007 Translation initiation factor IF-2
399 554 NCBIfam TIGR00231 small GTP-binding protein domain
399 554 InterPro IPR005225 Small GTP-binding protein domain
571 664 CDD cd03702 IF2_mtIF2_II
571 664 InterPro IPR044145 Translation initiation factor IF-2, domain II
797 894 FunFam G3DSA:2.40.30.10:FF:000008 Translation initiation factor IF-2
395 564 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile.
395 564 InterPro IPR000795 Translational (tr)-type GTP-binding domain
395 563 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
395 563 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
567 685 Gene3D G3DSA:2.40.30.10 Translation factors
3 893 Hamap MF_00100_B Translation initiation factor IF-2 [infB].
3 893 InterPro IPR000178 Translation initiation factor IF-2, bacterial-like
690 796 Gene3D G3DSA:3.40.50.10050 -
690 796 InterPro IPR036925 Translation initiation factor IF-2, domain 3 superfamily
105 894 PANTHER PTHR43381 TRANSLATION INITIATION FACTOR IF-2-RELATED
105 894 InterPro IPR015760 Translation initiation factor IF- 2
568 650 SUPERFAMILY SSF50447 Translation proteins
568 650 InterPro IPR009000 Translation protein, beta-barrel domain superfamily
168 218 Coils Coil Coil
846 868 ProSitePatterns PS01176 Initiation factor 2 signature.
846 868 InterPro IPR000178 Translation initiation factor IF-2, bacterial-like
797 894 Gene3D G3DSA:2.40.30.10 Translation factors
1 52 Pfam PF04760 Translation initiation factor IF-2, N-terminal region
1 52 InterPro IPR006847 Translation initiation factor IF-2, N-terminal
320 370 Pfam PF04760 Translation initiation factor IF-2, N-terminal region
320 370 InterPro IPR006847 Translation initiation factor IF-2, N-terminal
3 50 SUPERFAMILY SSF46955 Putative DNA-binding domain
3 50 InterPro IPR009061 Putative DNA-binding domain superfamily
392 566 FunFam G3DSA:3.40.50.300:FF:000019 Translation initiation factor IF-2
797 893 SUPERFAMILY SSF50447 Translation proteins
797 893 InterPro IPR009000 Translation protein, beta-barrel domain superfamily
93 228 MobiDBLite mobidb-lite consensus disorder prediction
673 802 SUPERFAMILY SSF52156 Initiation factor IF2/eIF5b, domain 3
673 802 InterPro IPR036925 Translation initiation factor IF-2, domain 3 superfamily

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 #4
0.644
Likely same site as P2Rank 5 3.1 Å 8 shared residues 89% of smaller site
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Surrounding area
Site 2 FPocket #1
0.319
Unusual size
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.091
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Surrounding area
Site 2 P2Rank #2
0.085
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Surrounding area
Site 3 P2Rank #3
0.082
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Surrounding area
Site 4 P2Rank #4
0.04
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Surrounding area
Site 5 P2Rank #5
0.037
Likely same site as FPocket 4 3.1 Å 8 shared residues 89% of smaller site
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Surrounding area
Residue sets
UniProt: Binding site:404-411
UniProt: Binding site:450-454
UniProt: Binding site:504-507
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_A0A0H3GY08
AlphaFold DB full sequence Viewing
ColabFold KP13_01100
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5GP PDB via homolog 363.2 Da · LogP -2.57 · TPSA 206.0 Open detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
FME PDB via homolog Detail RCSB PDB
GCP 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
5GP RCSB PDB P46199 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
DTT RCSB PDB G0S8G9 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
FES RCSB PDB P46199 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FME RCSB PDB P0A705 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
GCP RCSB PDB P39730 521.2 Da LogP -2.22 TPSA 289.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GNP RCSB PDB P0A705 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GSP RCSB PDB P46199 539.2 Da LogP -2.22 TPSA 282.0 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
LAC RCSB PDB G0S8G9 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)O
OHX RCSB PDB P39730 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
SPM RCSB PDB P46199 202.3 Da LogP -0.36 TPSA 76.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CNCCCN
SRY RCSB PDB P46199 581.6 Da LogP -7.74 TPSA 331.4 3 viol. ✓ Clean [H]/N=C(/N)\N[C@@H]1[C@H]([C@@H]([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.