KpKP13 Protein target profile

Bifunctional polymyxin resistance protein ArnA

Accession: KP13_00326

Gene: arnA AHE42234.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GX03
Length 661
Pocket druggability (P2Rank · AlphaFold DB model) 0.964
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 10 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 (%)
28.462 Lower values reduce human off-target concern.
Human E-value
5.84e-09
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
94.04 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) 0.964
Structure A0A0H3GX03
Pocket Pocket 1
Druggability (FPocket) 0.853
Structure A0A0H3GX03
Pocket Pocket 4
ColabFold model
P2Rank 0.954 · Pocket 1
FPocket 0.226 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 115 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKAVVFAYHDMGCTGIQALLDAGYDIAAIFTHPDNPGENHFFGSVARLAAEQGIPVWAPEDVNHPLWIERIREMKPDVLFSFYYRNLLGDEILNLAPKGAFNLHGSLLPKYRGRAPLNWVLVNGESETGVTLHRMVNRADAGDIVAQQAVAIGADDAALTLHRKLCAAATELLSRALPAILAGTTDERPQDHSQATYVGRRTPEDGRLDWELPAQTLHNLVRAVSDPWPGAFGYAGANKFIVWKSRVRHDLPAAKPGTVLSIAPLIVACQDGALEIVTGQTERGVYMQGAQLAQALGLVSGAVISSKPVVAIKRRTRVLILGVNGFIGNHLTERLLQDDNYEIYGLDIGSDAISRFLDCPRFHFVEGDISIHSEWIEYHIKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLKIIRDCVKYNKRIIFPSTSEVYGMCTDKNFDEDSSNLVVGPINKQRWIYSVSKQLLDRVIWAYGDKNGLKFTLFRPFNWMGPRLDNLNAARIGSSRAITQLILNLVEGSPIKLIEGGKQKRCFTDISDGIEALFRIIENKDGRCDGQIINIGNPDNEASIKELAEMLLACFERHPLRDRFPPFAGFREVESSDYYGKGYQDVEHRKPSIRNAKRCLNWEPKVEMEETVEHTLDFFLRTVELVDDKNP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

10
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0016742 Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0099619 Catalysis of the reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose.
  • GO:0099618 Catalysis of the reaction: UDP-alpha-D-glucuronate + NAD+ = UDP-beta-L-threo-pentopyranos-4-ulose + CO2 + NADH.
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
1 303 Gene3D G3DSA:3.40.50.12230 -
1 202 SUPERFAMILY SSF53328 Formyltransferase
1 202 InterPro IPR036477 Formyl transferase, N-terminal domain superfamily
314 660 FunFam G3DSA:3.40.50.720:FF:000197 Bifunctional polymyxin resistance protein ArnA
318 566 Pfam PF01370 NAD dependent epimerase/dehydratase family
318 566 InterPro IPR001509 NAD-dependent epimerase/dehydratase
202 294 Pfam PF02911 Formyl transferase, C-terminal domain
202 294 InterPro IPR005793 Formyl transferase, C-terminal
204 292 CDD cd08702 Arna_FMT_C
26 177 Pfam PF00551 Formyl transferase
26 177 InterPro IPR002376 Formyl transferase, N-terminal
316 652 PANTHER PTHR43245 BIFUNCTIONAL POLYMYXIN RESISTANCE PROTEIN ARNA
1 203 CDD cd08644 FMT_core_ArnA_N
1 660 Hamap MF_01166 Bifunctional polymyxin resistance protein ArnA [arnA].
1 660 InterPro IPR021168 Bifunctional polymyxin resistance protein, ArnA
314 660 Gene3D G3DSA:3.40.50.720 -
204 302 SUPERFAMILY SSF50486 FMT C-terminal domain-like
204 302 InterPro IPR011034 Formyl transferase-like, C-terminal domain superfamily
317 652 CDD cd05257 Arna_like_SDR_e
317 652 InterPro IPR045869 Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs
1 660 PIRSF PIRSF036506 MtRNA_frt_NDPSE
317 652 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
317 652 InterPro IPR036291 NAD(P)-binding domain 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 · P2Rank

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

Pocket 1 P2Rank #1
0.964
Likely same site as FPocket 4 6.6 Å 31 shared residues 82% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.939
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Surrounding area
Pocket 3 P2Rank #3
0.033
Likely same site as FPocket 24 2.1 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.026
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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 #4
0.853 Unusual size
Likely same site as P2Rank 1 6.6 Å 31 shared residues 82% of smaller site
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Surrounding area
Pocket 2 FPocket #24
0.252
Likely same site as P2Rank 3 2.1 Å 9 shared residues 100% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:104-104 Proton donor; for formyltransferase activity
UniProt: Active site:434-434 Proton acceptor; for decarboxylase activity
UniProt: Active site:619-619 Proton donor; for decarboxylase activity
UniProt: Binding site:114-114
UniProt: Binding site:136-140
UniProt: Binding site:347-347
UniProt: Binding site:368-369
UniProt: Binding site:393-393
UniProt: Binding site:398-398
UniProt: Binding site:432-433
UniProt: Binding site:460-460
UniProt: Binding site:492-492
UniProt: Binding site:526-535
UniProt: Binding site:613-613
UniProt: Site:102-102 Transition state stabilizer
UniProt: Site:140-140 Raises pKa of active site His
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_A0A0H3GX03
AlphaFold DB full sequence Viewing
ColabFold KP13_00326
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DTT PDB via homolog 154.3 Da · LogP -0.43 · TPSA 40.5 Open detail RCSB PDB
FME PDB via homolog Detail RCSB PDB
MOE PDB via homolog Detail RCSB PDB
PG5 PDB via homolog Detail RCSB PDB
UGA 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
DTT RCSB PDB P77398 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
FME RCSB PDB P23882 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
MOE RCSB PDB Q8ZJ80 75.1 Da LogP -1.01 TPSA 32.3 ✓ Ro5 ✓ Clean COCC[O-]
PG5 RCSB PDB Q81WH2 178.2 Da LogP 0.31 TPSA 36.9 ✓ Ro5 ✓ Clean COCCOCCOCCOC
UGA RCSB PDB P77398 580.3 Da LogP -4.70 TPSA 314.1 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.