Protein profile

VK055_0604

narK MFS nitrate/nitrite antiporter

Genome: KpATCC43816

Gene: narK2 AIK79227.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTE2

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Amino acids 460

Annotations 10

Features 48

PDB binders 2

Druggability 0.794

Overview

Basic information about this protein and its source genome.

Accession: VK055_0604
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: narK2 AIK79227.1
Status: annotated
Amino acids: 460
Structure source: AlphaFold + ColabFold

GO:0015707 The directed movement of nitrite into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0015113 Enables the transfer of nitrite (NO2-) ions from one side of a membrane to the other. GO:0015706 The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015112 Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 79.476
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 93.21

Selected Druggability evidence

AlphaFold / UniProt model

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 0.794

Structure A0A0H3GTE2

Pocket Pocket 31

P2Rank 0.968

Structure A0A0H3GTE2

Pocket Pocket 1

ColabFold model

FPocket 0.867 · Pocket 19

P2Rank 0.95 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 108 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

GO:0015707 The directed movement of nitrite into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0015113 Enables the transfer of nitrite (NO2-) ions from one side of a membrane to the other.
GO:0015706 The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0015112 Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0015291 Enables the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy, not direct ATP coupling. Secondary active transporters include symporters and antiporters.
GO:0042128 The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.

Sequence Features

Domain/signature hits from InterPro and related databases.

48 records

Show feature table

Start	End	DB	Term	Name
128	150	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
36	452	CDD	cd17341	MFS_NRT2_like
36	452	InterPro	IPR044772	Nitrate transporter
11	454	PANTHER	PTHR23515	HIGH-AFFINITY NITRATE TRANSPORTER 2.3
11	454	InterPro	IPR044772	Nitrate transporter
43	419	Pfam	PF07690	Major Facilitator Superfamily
43	419	InterPro	IPR011701	Major facilitator superfamily
396	418	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
233	252	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
214	232	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
288	306	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
307	317	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
178	200	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
171	194	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
36	60	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
346	375	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
277	287	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
72	90	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
195	213	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
318	340	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
313	335	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	460	Gene3D	G3DSA:1.20.1250.20	MFS general substrate transporter like domains
1	460	InterPro	IPR036259	MFS transporter superfamily
345	367	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
341	345	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
36	58	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
419	437	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
128	150	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
253	276	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
91	101	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
34	415	NCBIfam	TIGR00886	NarK family nitrate/nitrite MFS transporter
34	415	InterPro	IPR004737	Nitrate transporter NarK/NarU-like
376	395	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
102	122	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
123	127	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
61	71	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
438	454	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
14	458	SUPERFAMILY	SSF103473	MFS general substrate transporter
14	458	InterPro	IPR036259	MFS transporter superfamily
1	35	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
455	460	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
99	121	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
213	232	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	460	FunFam	G3DSA:1.20.1250.20:FF:000024	Nitrite extrusion protein NarK
401	418	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
151	170	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
254	276	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
433	455	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GTE2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0604	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
31				0.794
14				0.726
1				0.299

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	33.83	0.948
2	7.94	0.422
3	2.02	0.044
4	1.55	0.023
5	1.12	0.008

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
19				0.867
7				0.71
12				0.665

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	28.74	0.927
2	9.68	0.52
3	2.61	0.075
4	2.14	0.05
5	1.26	0.012

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

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
OLA	4U4T	P10903	282.5 Da LogP 6.11 TPSA 37.3	1 viol.	✓ Clean	`CCCCCCCC\C=C/CCCCCCCC(=O)O`
OLC	4U4T	P10903	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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).

No ChEMBL hits found through similar proteins.

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
ZINC1501016272	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC1501016273	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC1501016315	1.000	314.5 Da LogP 3.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC1501016316	1.000	314.5 Da LogP 3.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC2038077522	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2038077523	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC221534416	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@@H](O)CO`
ZINC32840893	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840894	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840895	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840896	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840901	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840902	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840903	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840904	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC64633397	1.000	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC725433050	1.000	342.5 Da LogP 4.53 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC725433052	1.000	342.5 Da LogP 4.53 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC98208566	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@H](O)CO`
ZINC32840885	0.943	300.4 Da LogP 3.36 TPSA 66.8	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2053467566	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC=CCC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2053467567	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC=CCC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC29045599	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4557100	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4557101	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC5819989	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC5819990	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC85425978	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC1531062	0.917	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCC(=O)O`
ZINC2504617	0.917	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCCC(=O)O`
ZINC32786138	0.917	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCC(=O)O`
ZINC4529321	0.917	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)O`
ZINC5260769	0.917	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCCC(=O)O`
ZINC29045446	0.892	352.5 Da LogP 4.47 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\C/C=C\CCCCC(=O)OC[C@@H](O)CO`
ZINC13532428	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC13532431	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC13532435	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC13546140	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC13546141	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC2296552808	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC2296552809	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)CC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC33832849	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC35052109	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4411072	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC4411074	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)CC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC100503477	0.824	260.4 Da LogP 2.41 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840884	0.824	302.5 Da LogP 3.58 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840889	0.824	316.5 Da LogP 3.97 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840890	0.824	316.5 Da LogP 3.97 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC77313111	0.824	344.5 Da LogP 4.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO`

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.