Protein profile

KP13_04711

Respiratory nitrate reductase 1 beta chain

Genome: KpKP13

Gene: narH AHE44024.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GV03

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Amino acids 511

Annotations 12

Features 25

PDB binders 16

Druggability 0.454

Overview

Basic information about this protein and its source genome.

Accession: KP13_04711
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: narH AHE44024.1
Status: annotated
Amino acids: 511
Structure source: AlphaFold + ColabFold

1.7.5.1

GO:0009325 An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor. GO:0042126 The chemical reactions and pathways involving nitrates, inorganic or organic salts and esters of nitric acid. GO:0008940 Catalysis of the reaction: nitrite + acceptor = nitrate + reduced acceptor. 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:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.

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 (%): 96.282
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 97.43

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 0.454

Structure A0A0H3GV03

Pocket Pocket 11

P2Rank 0.182

Structure A0A0H3GV03

Pocket Pocket 1

ColabFold model

FPocket 0.503 · Pocket 12

P2Rank 0.182 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 283 / 4744 genomes with a hit

Normalized 0.06

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1.7.5.1

Gene Ontology (GO)

GO:0009325 An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor.
GO:0042126 The chemical reactions and pathways involving nitrates, inorganic or organic salts and esters of nitric acid.
GO:0008940 Catalysis of the reaction: nitrite + acceptor = nitrate + reduced acceptor.
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:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
GO:0046872 Binding to a metal ion.
GO:0160182 Catalysis of the reaction: a quinol + nitrate = a quinone + H2O + nitrite.
GO:0019645 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors other than oxygen to generate a transmembrane electrochemical gradient.
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.

25 records

Show feature table

Start	End	DB	Term	Name
1	508	PANTHER	PTHR43518	NITRATE REDUCTASE BETA SUBUNIT
3	367	CDD	cd10557	NarH_beta-like
3	367	InterPro	IPR006547	Nitrate reductase, beta subunit
5	90	FunFam	G3DSA:3.30.70.20:FF:000010	Respiratory nitrate reductase beta subunit
362	434	FunFam	G3DSA:1.10.3650.10:FF:000001	Respiratory nitrate reductase subunit beta
358	436	Pfam	PF14711	Respiratory nitrate reductase beta C-terminal
358	436	InterPro	IPR029263	Respiratory nitrate reductase beta, C-terminal
7	35	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
7	35	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
175	271	Pfam	PF13247	4Fe-4S dicluster domain
175	271	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
241	362	FunFam	G3DSA:3.30.70.20:FF:000008	Respiratory nitrate reductase beta subunit
1	492	NCBIfam	TIGR01660	nitrate reductase subunit beta
1	492	InterPro	IPR006547	Nitrate reductase, beta subunit
362	434	Gene3D	G3DSA:1.10.3650.10	nitrate reductase domain like
362	434	InterPro	IPR038262	Nitrate reductase beta, C-terminal domain superfamily
241	361	Gene3D	G3DSA:3.30.70.20	-
1	503	SUPERFAMILY	SSF54862	4Fe-4S ferredoxins
5	91	Gene3D	G3DSA:3.30.70.20	-
156	240	Gene3D	G3DSA:3.30.70.20	-
207	236	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
207	236	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
174	205	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
174	205	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
157	240	FunFam	G3DSA:3.30.70.20:FF:000005	Respiratory nitrate reductase beta subunit

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_A0A0H3GV03	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04711	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
11				0.454
10				0.347

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	4.18	0.17
2	3.01	0.099
3	2.74	0.083
4	2.63	0.076
5	1.74	0.031

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
12				0.503

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	3.49	0.128
2	3.39	0.121
3	3.34	0.119
4	3.12	0.105
5	2.88	0.092

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.

66 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
3PH	1Q16	P11349	705.0 Da LogP 12.07 TPSA 119.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O…`
4MO	4V4C	P80564	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+4]`
6MO	1Q16	P11349	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+6]`
AGA	1Q16	P11349	455.5 Da LogP 1.85 TPSA 151.7	✓ Ro5	✓ Clean	`CCCCCCCC(=O)O[C@H](COC(=O)CCCC)COP(=O)([O-])OC[…`
BSY	5CHC	G8QM54	128.0 Da LogP -2.25 TPSA 60.4	✓ Ro5	✓ Clean	`O[Se](=O)[O-]`
BTT	4V4E	P80564	142.1 Da LogP 0.51 TPSA 80.9	✓ Ro5	Alert	`c1c(c(cc(c1O)O)O)O`
CDL	1KQF	P0AAJ3	1464.1 Da LogP 23.31 TPSA 242.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…`
F3S	1Q16	P11349	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
HQO	1KQG	P0AAJ3	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(c2ccccc2[n+]1[O-])O`
MD1	1Q16	P11349	740.6 Da LogP -2.13 TPSA 358.0	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
MGD	1R27	P11349	740.6 Da LogP -2.06 TPSA 346.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
MO	1R27	P11349	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo]`
O	6CZ8	Q7WTT9	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
PCI	1Y4Z	P11349	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O`
PG5	6CZ8	Q7WTT9	178.2 Da LogP 0.31 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOC`
PYG	4V4D	P80564	126.1 Da LogP 0.80 TPSA 60.7	✓ Ro5	Alert	`c1cc(c(c(c1)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).

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
ZINC1529471	1.000	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC1529909	1.000	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(O)c2ccccc2[n+]1[O-]`
ZINC1692489	1.000	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC36178999	1.000	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	1.000	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC4530388	1.000	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5701172	1.000	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	1.000	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC5820131	0.971	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.971	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC225408	0.900	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(O)c(Cl)c1Cl`
ZINC154748	0.818	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	Alert	`Oc1c(O)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC102191119	0.792	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.792	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC4521879	0.743	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC34764844	0.733	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC102190506	0.727	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	0.727	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC27416437	0.705	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.705	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC137999083	0.700	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC42851452	0.700	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC62624856	0.700	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC62624861	0.700	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC8218993	0.700	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC8219000	0.700	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC13543394	0.689	455.4 Da LogP 2.15 TPSA 171.7	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](N)C(=O)…`
ZINC140264883	0.688	223.3 Da LogP -0.43 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCON`
ZINC143705779	0.688	443.5 Da LogP -0.34 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33358855	0.688	207.3 Da LogP -0.36 TPSA 62.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCN`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44583772	0.688	356.5 Da LogP 0.66 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCS`
ZINC5024003	0.688	251.3 Da LogP -0.34 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCN`
ZINC575432090	0.688	355.4 Da LogP -0.38 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCON`
ZINC575432265	0.688	399.5 Da LogP -0.36 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC71254558	0.688	444.6 Da LogP 0.70 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC71254563	0.688	488.6 Da LogP 0.71 TPSA 92.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC80685077	0.688	427.5 Da LogP -0.28 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC83253927	0.688	400.5 Da LogP 0.68 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253930	0.688	224.3 Da LogP 0.61 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCS`
ZINC83253936	0.688	383.5 Da LogP -0.29 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC90556279	0.688	295.4 Da LogP -0.33 TPSA 81.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCN`
ZINC90556286	0.688	312.4 Da LogP 0.65 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCS`
ZINC90556287	0.688	268.4 Da LogP 0.63 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCS`
ZINC96503353	0.688	471.6 Da LogP -0.26 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCN`

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.