Protein profile

KP13_02920

Na(+)-translocating NADH-quinone reductase subunit F

Genome: KpKP13

Gene: nqrF AHE46196.1 Structure source: Experimental + ColabFold UniProt A6T526

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Amino acids 407

Annotations 6

Features 47

PDB binders 7

Druggability 0.966

Overview

Basic information about this protein and its source genome.

Accession: KP13_02920
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: nqrF AHE46196.1
Status: annotated
Amino acids: 407
Structure source: Experimental + ColabFold

GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule. GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 26.531
Human E-value: 2.27e-08
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.71

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 0.966

Structure 7QTY

Pocket Pocket 1

P2Rank 0.576

Structure 7QU0

Pocket Pocket 1

ColabFold model

FPocket 0.828 · Pocket 1

P2Rank 0.592 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 417 / 4744 genomes with a hit

Normalized 0.088

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.

Sequence Features

Domain/signature hits from InterPro and related databases.

47 records

Show feature table

Start	End	DB	Term	Name
123	405	CDD	cd06188	NADH_quinone_reductase
126	264	Gene3D	G3DSA:2.40.30.10	Translation factors
43	115	Pfam	PF00111	2Fe-2S iron-sulfur cluster binding domain
43	115	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
204	266	Pfam	PF00970	Oxidoreductase FAD-binding domain
204	266	InterPro	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
2	24	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
126	264	FunFam	G3DSA:2.40.30.10:FF:000064	Na(+)-translocating NADH-quinone reductase subunit F
275	393	FunFam	G3DSA:3.40.50.80:FF:000014	Na(+)-translocating NADH-quinone reductase subunit F
4	23	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	407	Hamap	MF_00430	Na(+)-translocating NADH-quinone reductase subunit F [nqrF].
1	407	InterPro	IPR010205	Na(+)-translocating NADH-quinone reductase subunit F
275	393	Gene3D	G3DSA:3.40.50.80	-
275	393	InterPro	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
105	272	SUPERFAMILY	SSF63380	Riboflavin synthase domain-like
105	272	InterPro	IPR017938	Riboflavin synthase-like beta-barrel
1	23	SignalP_EUK	SignalP-TM	SignalP-TM
23	407	PANTHER	PTHR43644	NA(+)-TRANSLOCATING NADH-QUINONE REDUCTASE SUBUNIT
37	124	SUPERFAMILY	SSF54292	2Fe-2S ferredoxin-like
37	124	InterPro	IPR036010	2Fe-2S ferredoxin-like superfamily
34	125	Gene3D	G3DSA:3.10.20.30	-
34	125	InterPro	IPR012675	Beta-grasp domain superfamily
129	269	ProSiteProfiles	PS51384	Ferredoxin reductase-type FAD binding domain profile.
129	269	InterPro	IPR017927	FAD-binding domain, ferredoxin reductase-type
373	381	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
373	381	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
242	251	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
242	251	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
209	216	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
209	216	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
276	295	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
276	295	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
314	325	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
314	325	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
32	407	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
3	407	NCBIfam	TIGR01941	NADH:ubiquinone reductase (Na(+)-transporting) subunit F
3	407	InterPro	IPR010205	Na(+)-translocating NADH-quinone reductase subunit F
32	126	ProSiteProfiles	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
32	126	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
1	31	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	407	PIRSF	PIRSF000044	Cis_Diol_DH_RD
24	31	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
255	402	SUPERFAMILY	SSF52343	Ferredoxin reductase-like, C-terminal NADP-linked domain
255	402	InterPro	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
277	386	Pfam	PF00175	Oxidoreductase NAD-binding domain
277	386	InterPro	IPR001433	Oxidoreductase FAD/NAD(P)-binding

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 7QTY	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
PDB 7QU0	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Loaded
ColabFold KP13_02920	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
1				0.966

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				0.828
12				0.264

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	8.94	0.479
2	4.96	0.224
3	4.21	0.172
4	3.55	0.131
5	1.47	0.02

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
BTB	4WQM	Q03304	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
DGG	1CQX	P39662	735.0 Da LogP 9.75 TPSA 148.8	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…`
ECN	3OZV	P39662	381.7 Da LogP 5.80 TPSA 27.1	1 viol.	✓ Clean	`c1cc(ccc1COC(Cn2ccnc2)c3ccc(cc3Cl)Cl)Cl`
FDA	1TVC	P22868	787.6 Da LogP -1.75 TPSA 363.3	3 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
FES	5OGX	A0A076MZ01	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
KKK	3OZW	P39662	531.4 Da LogP 4.21 TPSA 69.1	1 viol.	Alert	`CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@H]3CO[C@](O3)(Cn…`
X89	3OZU	P39662	416.1 Da LogP 6.45 TPSA 27.1	1 viol.	✓ Clean	`c1cc(c(cc1Cl)Cl)CO[C@@H](Cn2ccnc2)c3ccc(cc3Cl)Cl`

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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC102191119	0.824	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	0.824	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)…`
ZINC28568236	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@@]2(Cn3ccnc3)OC[C@H](COc3ccc(N4CCNCC…`
ZINC31416683	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@]2(Cn3ccnc3)OC[C@@H](COc3ccc(N4CCNCC…`
ZINC38944078	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@]2(Cn3ccnc3)OC[C@H](COc3ccc(N4CCNCC4…`
ZINC38944080	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@@]2(Cn3ccnc3)OC[C@@H](COc3ccc(N4CCNC…`
ZINC1532199	0.729	297.2 Da LogP 4.13 TPSA 27.1	✓ Ro5	✓ Clean	`C=CCO[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC1532200	0.729	297.2 Da LogP 4.13 TPSA 27.1	✓ Ro5	✓ Clean	`C=CCO[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC95918118	0.673	312.8 Da LogP 4.49 TPSA 27.1	✓ Ro5	✓ Clean	`Clc1ccc(CO[C@H](Cn2ccnc2)c2ccccc2)cc1`
ZINC95918119	0.673	312.8 Da LogP 4.49 TPSA 27.1	✓ Ro5	✓ Clean	`Clc1ccc(CO[C@@H](Cn2ccnc2)c2ccccc2)cc1`
ZINC102191158	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC14880758	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OC[…`
ZINC14880760	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OC[C…`
ZINC53683910	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[…`
ZINC62592202	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC62592203	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC62592204	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC…`
ZINC96094841	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC849188212	0.654	327.2 Da LogP 4.13 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)C(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188213	0.654	327.2 Da LogP 4.13 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)C(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC38334168	0.649	407.3 Da LogP 2.43 TPSA 79.7	✓ Ro5	✓ Clean	`CS(=O)(=O)OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc…`
ZINC198375289	0.635	299.2 Da LogP 3.49 TPSA 44.1	✓ Ro5	✓ Clean	`CC(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC198375301	0.635	299.2 Da LogP 3.49 TPSA 44.1	✓ Ro5	✓ Clean	`CC(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC5349880	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O…`
ZINC5349883	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1…`
ZINC638711	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1)…`
ZINC638717	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1…`
ZINC297645	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297649	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297652	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297656	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC102190506	0.614	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	0.614	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC4217243	0.605	367.2 Da LogP 3.11 TPSA 45.5	✓ Ro5	✓ Clean	`C#CCOC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC390893	0.604	257.1 Da LogP 2.92 TPSA 38.0	✓ Ro5	✓ Clean	`O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC390894	0.604	257.1 Da LogP 2.92 TPSA 38.0	✓ Ro5	✓ Clean	`O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC21988957	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2CO[C@](Cn3ccnc3)(c3ccc(…`
ZINC22057057	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2CO[C@@](Cn3ccnc3)(c3cc…`
ZINC22057060	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2CO[C@](Cn3ccnc3)(c3ccc…`
ZINC6088320	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2CO[C@@](Cn3ccnc3)(c3ccc…`
ZINC849187659	0.600	325.2 Da LogP 3.88 TPSA 44.1	✓ Ro5	✓ Clean	`O=C(O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl)C1CC1`
ZINC849187660	0.600	325.2 Da LogP 3.88 TPSA 44.1	✓ Ro5	✓ Clean	`O=C(O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl)C1CC1`
ZINC27416437	0.596	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	0.596	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC36178999	0.593	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.593	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC849188227	0.589	341.2 Da LogP 4.52 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188228	0.589	341.2 Da LogP 4.52 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188301	0.589	355.3 Da LogP 4.91 TPSA 44.1	✓ Ro5	✓ Clean	`CCC(CC)C(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`

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.