Protein profile

KP13_04511

Respiratory nitrate reductase 2 beta chain

Genome: KpKP13

Gene: AHE44387.1 narY Structure source: AlphaFold + ColabFold UniProt A0A2V3KBT0

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Amino acids 514

Annotations 12

Features 25

PDB binders 13

Druggability 0.613

Overview

Basic information about this protein and its source genome.

Accession: KP13_04511
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44387.1 narY
Status: annotated
Amino acids: 514
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 (%): 89.883
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 94.46

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 0.613

Structure A0A2V3KBT0

Pocket Pocket 5

P2Rank 0.151

Structure A0A2V3KBT0

Pocket Pocket 1

ColabFold model

FPocket 0.131 · Pocket 30

P2Rank 0.184 · 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	493	NCBIfam	TIGR01660	nitrate reductase subunit beta
1	493	InterPro	IPR006547	Nitrate reductase, beta subunit
3	367	CDD	cd10557	NarH_beta-like
3	367	InterPro	IPR006547	Nitrate reductase, beta subunit
175	271	Pfam	PF13247	4Fe-4S dicluster domain
175	271	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
1	506	PANTHER	PTHR43518	NITRATE REDUCTASE BETA SUBUNIT
362	435	Gene3D	G3DSA:1.10.3650.10	nitrate reductase domain like
362	435	InterPro	IPR038262	Nitrate reductase beta, C-terminal domain superfamily
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
5	90	FunFam	G3DSA:3.30.70.20:FF:000010	Respiratory nitrate reductase beta subunit
157	240	FunFam	G3DSA:3.30.70.20:FF:000005	Respiratory nitrate reductase beta subunit
241	362	FunFam	G3DSA:3.30.70.20:FF:000008	Respiratory nitrate reductase beta subunit
5	73	Gene3D	G3DSA:3.30.70.20	-
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
358	436	Pfam	PF14711	Respiratory nitrate reductase beta C-terminal
358	436	InterPro	IPR029263	Respiratory nitrate reductase beta, C-terminal
158	240	Gene3D	G3DSA:3.30.70.20	-
241	361	Gene3D	G3DSA:3.30.70.20	-
362	435	FunFam	G3DSA:1.10.3650.10:FF:000001	Respiratory nitrate reductase subunit beta
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
1	501	SUPERFAMILY	SSF54862	4Fe-4S ferredoxins

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_A0A2V3KBT0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04511	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
5				0.613
2				0.447

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	3.95	0.156
2	3.15	0.107
3	2.92	0.093
4	2.82	0.088
5	1.69	0.029

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	3.45	0.125
2	3.07	0.102
3	3.01	0.099
4	2.76	0.084
5	2.47	0.068

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.

63 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…`
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-]`
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	7B04	Q1PZD5	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	7B04	Q1PZD5	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	6CZ8	Q7WTT9	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	6CZ8	Q7WTT9	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`

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`
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`
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`
ZINC34764844	0.733	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC102191119	0.708	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	0.708	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)…`
ZINC36178999	0.705	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.705	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
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`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
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`
ZINC90556280	0.688	339.4 Da LogP -0.31 TPSA 90.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCN`
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`
ZINC34541308	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC5820131	0.682	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.682	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC4521879	0.650	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC113456917	0.647	220.3 Da LogP 1.48 TPSA 36.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOC`
ZINC146934560	0.647	397.5 Da LogP -0.03 TPSA 85.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCNCCOCCOCCOCCOC`
ZINC218810670	0.647	308.4 Da LogP 1.52 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOCCOCCOC`
ZINC33506597	0.647	309.4 Da LogP -0.06 TPSA 67.4	✓ Ro5	✓ Clean	`COCCOCCOCCNCCOCCOCCOC`
ZINC34303570	0.647	264.4 Da LogP 1.50 TPSA 46.2	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOCCOC`
ZINC3860567	0.647	323.4 Da LogP 0.28 TPSA 58.6	✓ Ro5	✓ Clean	`COCCOCCN(CCOCCOC)CCOCCOC`
ZINC5701149	0.647	221.3 Da LogP -0.10 TPSA 49.0	✓ Ro5	✓ Clean	`COCCOCCNCCOCCOC`
ZINC104869865	0.630	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=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.