Protein target profile

VK055_3123

biotin operon repressor

Genome: KpATCC43816 Gene: AIK81700.1 3D evidence: Experimental + ColabFold model UniProt A0A0W7ZMT5
Length 320
Pocket druggability 0.976
Direct ligand evidence 0 57 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.

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 (%)
32.258 Lower values reduce human off-target concern.
Human E-value
1.07e-06
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
84.688 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
93.59 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.976
Structure 8F8U
Pocket Pocket 1
P2Rank 0.156
Structure 8F8U
Pocket Pocket 1
ColabFold model
FPocket 0.928 · Pocket 1
P2Rank 0.419 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 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.

MKDHTIPLTLISILADGEFHSGEQLGEQLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIHLLDEKKISQEIDHGRVTVLPVIDSTNQYLLDRLDELTSGDACVAEYQQAGRGRRGRKWFSPFGANLYLSMYWRLEQGPAAAIGLSLVIGIVIAEVLQQLGAEQVRVKWPNDIYLQDRKLSGILVELTGKTGDAAQIVSGAGINLVMRRVESDVVNQGWISLQEAGVVIDRNLLAARLIKELRLGLELFEQEGLAPYLPRWEKLDNFIHRPVKLIIGDKEIYGISRGIDAQGALLLEQDGVIKAWVGGEISLRSAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0004077 Catalysis of the reaction: ATP + biotin + L-lysyl-[protein] = AMP + diphosphate + H+ + N(6)-biotinyl-L-lysyl-[protein].
  • GO:0036211 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
7 317 Hamap MF_00978 Bifunctional ligase/repressor BirA [birA].
7 317 InterPro IPR030855 Bifunctional ligase/repressor BirA
84 208 Pfam PF03099 Biotin/lipoate A/B protein ligase family
84 208 InterPro IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
274 317 Pfam PF02237 Biotin protein ligase C terminal domain
274 317 InterPro IPR003142 Biotin protein ligase, C-terminal
66 254 ProSiteProfiles PS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.
66 254 InterPro IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
14 303 PANTHER PTHR12835 BIOTIN PROTEIN LIGASE
5 60 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
5 60 InterPro IPR036390 Winged helix DNA-binding domain superfamily
81 317 NCBIfam TIGR00121 biotin--[acetyl-CoA-carboxylase] ligase
81 317 InterPro IPR004408 Biotin--acetyl-CoA-carboxylase ligase
1 64 Gene3D G3DSA:1.10.10.10 -
1 64 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
271 320 Gene3D G3DSA:2.30.30.100 -
271 320 FunFam G3DSA:2.30.30.100:FF:000030 Bifunctional ligase/repressor BirA
78 268 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
78 268 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
65 270 FunFam G3DSA:3.30.930.10:FF:000050 Bifunctional ligase/repressor BirA
1 64 FunFam G3DSA:1.10.10.10:FF:000356 Bifunctional ligase/repressor BirA
65 270 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
65 270 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
80 253 CDD cd16442 BPL
80 253 InterPro IPR004408 Biotin--acetyl-CoA-carboxylase ligase
7 73 NCBIfam TIGR00122 biotin operon repressor
7 73 InterPro IPR004409 Biotin operon repressor, helix-turn-helix domain
10 58 Pfam PF08279 HTH domain
10 58 InterPro IPR013196 Helix-turn-helix, type 11
271 317 SUPERFAMILY SSF50037 C-terminal domain of transcriptional repressors
271 317 InterPro IPR008988 Transcriptional repressor, C-terminal

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 #1
0.976
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #2
0.715
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.156
Show in viewer
Surrounding area
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 1

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
PDB 8F8U
X-ray 2.85 Å A,B
100.0% 1-320
Viewing
PDB 8FI3
X-ray 2.90 Å A,B
100.0% 1-320
Loaded
ColabFold VK055_3123
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.

57 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ADN PDB via homolog 267.2 Da · LogP -1.98 · TPSA 139.5 Open detail RCSB PDB
BQX PDB via homolog Detail RCSB PDB
BT5 PDB via homolog Detail RCSB PDB
N3G PDB via homolog Detail RCSB PDB
POP 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
ADN RCSB PDB O57883 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BQX RCSB PDB Q2G258 526.6 Da LogP -0.34 TPSA 198.1 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)CCCCNS(=O)(=O)NC(=O)NCCCC[C@H…
BT5 RCSB PDB O57883 573.5 Da LogP -0.59 TPSA 233.3 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
N3G RCSB PDB A0A3A5LBF0 511.6 Da LogP -0.13 TPSA 186.0 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)CCCCNS(=O)(=O)NC(=O)CCCC[C@H]…
POP RCSB PDB O57883 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.