Protein profile

VK055_3123

biotin operon repressor

Genome: KpATCC43816

Gene: AIK81700.1 Structure source: Experimental + ColabFold UniProt A0A0W7ZMT5

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Amino acids 320

Annotations 7

Features 31

PDB binders 5

Druggability 0.976

Overview

Basic information about this protein and its source genome.

Accession: VK055_3123
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81700.1
Status: annotated
Amino acids: 320
Structure source: Experimental + ColabFold

6.3.4.15

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).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 32.258
Human E-value: 1.07e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 84.688
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.59

Selected Druggability evidence

PDB experimental structure

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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

Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

6.3.4.15

Gene Ontology (GO)

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

2 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 8F8U	X-ray	2.85 Å	A,B	100.0% 1-320	PDBe RCSB PDBj File	Viewing
PDB 8FI3	X-ray	2.90 Å	A,B	100.0% 1-320	PDBe RCSB PDBj File	Loaded
ColabFold VK055_3123	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
28				0.823
1				0.708

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	4.42	0.186
2	4.08	0.164
3	3.95	0.157
4	2.35	0.061

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.928
22				0.329

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				7.4	0.387
2				2.19	0.052

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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
ADN	2EJF	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	6NDL	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	1WQW	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	6ORU	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	2DKG	O57883	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
BTX	A0A0E7NXW5	7.52	559.5 Da LogP -0.11 TPSA 216.2	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
CHEMBL3701289	A0A0E7NXW5	6.18	470.6 Da LogP 1.75 TPSA 141.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2CCCCn1cc(CCCCC[C@@H]2SC[C@@H]3NC(…`

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
ZINC13783922	0.612	392.2 Da LogP -0.77 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(I)cn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@…`
ZINC14806687	0.612	392.2 Da LogP -0.77 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(I)cn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H…`
ZINC17418569	0.612	345.2 Da LogP -0.61 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(Br)cn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC2516039	0.612	392.2 Da LogP -0.77 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(I)cn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H…`
ZINC26737828	0.612	392.2 Da LogP -0.77 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(I)cn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]…`
ZINC26740660	0.612	345.2 Da LogP -0.61 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(Br)cn2[C@@H]1O[C@H](CO)[C@H](O)[C@@…`
ZINC26740665	0.612	345.2 Da LogP -0.61 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(Br)cn2[C@@H]1O[C@H](CO)[C@H](O)[C@H…`
ZINC27646915	0.612	392.2 Da LogP -0.77 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(I)cn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]…`
ZINC34441457	0.612	284.2 Da LogP -1.24 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(F)cn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC4743791	0.612	346.1 Da LogP -1.22 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(Br)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3…`
ZINC4743792	0.612	346.1 Da LogP -1.22 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(Br)c2ncn([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]…`
ZINC4743793	0.612	346.1 Da LogP -1.22 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(Br)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4743794	0.612	346.1 Da LogP -1.22 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(Br)c2ncn([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC49785288	0.612	345.2 Da LogP -0.61 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(Br)cn2[C@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC5010881	0.612	295.3 Da LogP -1.92 TPSA 152.7	✓ Ro5	✓ Clean	`NCc1cn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2ncnc…`
ZINC5010882	0.612	295.3 Da LogP -1.92 TPSA 152.7	✓ Ro5	✓ Clean	`NCc1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2ncn…`
ZINC5010884	0.612	295.3 Da LogP -1.92 TPSA 152.7	✓ Ro5	✓ Clean	`NCc1cn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2ncn…`
ZINC5010885	0.612	295.3 Da LogP -1.92 TPSA 152.7	✓ Ro5	✓ Clean	`NCc1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2nc…`
ZINC5161614	0.612	345.2 Da LogP -0.61 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(Br)cn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC5161616	0.612	392.2 Da LogP -0.77 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1ncnc2c1c(I)cn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC6585262	0.604	283.2 Da LogP -2.44 TPSA 149.6	✓ Ro5	✓ Clean	`N=c1c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c2n…`
ZINC31544818	0.600	288.7 Da LogP 0.07 TPSA 93.3	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c(Cl)ncnc32)[C@H](F)[C@@H…`
ZINC31728961	0.600	300.7 Da LogP -0.72 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1cc(Cl)c2ncn([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC31728964	0.600	300.7 Da LogP -0.72 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1cc(Cl)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC38981496	0.600	288.7 Da LogP 0.07 TPSA 93.3	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c(Cl)ncnc32)[C@@H](F)[C@@…`
ZINC44168239	0.600	281.3 Da LogP -2.43 TPSA 171.4	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3N…`
ZINC53277583	0.600	300.7 Da LogP -0.72 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1cc(Cl)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3…`
ZINC53277584	0.600	300.7 Da LogP -0.72 TPSA 126.7	✓ Ro5	✓ Clean	`Nc1cc(Cl)c2ncn([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]…`
ZINC1320093	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3cncnc32)[C@@H](O)[C@@H]1O`
ZINC13542583	0.596	258.2 Da LogP -2.82 TPSA 156.8	✓ Ro5	✓ Clean	`NC(=O)c1c(N)ncn1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]…`
ZINC13548142	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3cncnc32)[C@H](O)[C@H]1O`
ZINC3814314	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3cncnc32)[C@H](O)[C@@H]1O`
ZINC4758247	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3cncnc32)[C@H](O)[C@@H]1O`
ZINC4758248	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@@H](n2cnc3cncnc32)[C@H](O)[C@@H]1O`
ZINC4758249	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3cncnc32)[C@@H](O)[C@@H]1O`
ZINC4758250	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@@H](n2cnc3cncnc32)[C@@H](O)[C@@H]1O`
ZINC4878189	0.596	258.2 Da LogP -2.82 TPSA 156.8	✓ Ro5	✓ Clean	`NC(=O)c1c(N)ncn1[C@H]1O[C@@H](CO)[C@@H](O)[C@H]…`
ZINC4878191	0.596	258.2 Da LogP -2.82 TPSA 156.8	✓ Ro5	✓ Clean	`NC(=O)c1c(N)ncn1[C@@H]1O[C@@H](CO)[C@@H](O)[C@H…`
ZINC4878196	0.596	258.2 Da LogP -2.82 TPSA 156.8	✓ Ro5	✓ Clean	`NC(=O)c1c(N)ncn1[C@H]1O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC4878200	0.596	258.2 Da LogP -2.82 TPSA 156.8	✓ Ro5	✓ Clean	`NC(=O)c1c(N)ncn1[C@@H]1O[C@@H](CO)[C@@H](O)[C@@…`
ZINC65748061	0.596	252.2 Da LogP -1.56 TPSA 113.5	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3cncnc32)[C@@H](O)[C@H]1O`
ZINC13518964	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1842158	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4806442	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.595	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)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.