Protein profile

KP13_05031

Fumarate nitrate reduction regulatory protein

Genome: KpKP13

Gene: fnr AHE44794.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMU3

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Amino acids 250

Annotations 8

Features 32

PDB binders 6

Druggability 0.511

Overview

Basic information about this protein and its source genome.

Accession: KP13_05031
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: fnr AHE44794.1
Status: annotated
Amino acids: 250
Structure source: AlphaFold + ColabFold

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0032993 A macromolecular complex containing both protein and DNA molecules. 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): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 90.06

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 0.511

Structure A0A0H3GMU3

Pocket Pocket 1

P2Rank 0.882

Structure A0A0H3GMU3

Pocket Pocket 1

ColabFold model

FPocket 0.235 · Pocket 14

P2Rank 0.845 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 146 / 4744 genomes with a hit

Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0032993 A macromolecular complex containing both protein and DNA molecules.
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:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records

Show feature table

Start	End	DB	Term	Name
34	144	CDD	cd00038	CAP_ED
34	144	InterPro	IPR000595	Cyclic nucleotide-binding domain
51	132	Pfam	PF00027	Cyclic nucleotide-binding domain
51	132	InterPro	IPR000595	Cyclic nucleotide-binding domain
209	224	PRINTS	PR00034	CRP bacterial regulatory protein HTH signature
209	224	InterPro	IPR012318	Crp-type HTH domain
193	209	PRINTS	PR00034	CRP bacterial regulatory protein HTH signature
193	209	InterPro	IPR012318	Crp-type HTH domain
165	250	Gene3D	G3DSA:1.10.10.10	-
165	250	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
30	151	SMART	SM00100	cnmp_10
30	151	InterPro	IPR000595	Cyclic nucleotide-binding domain
50	244	PANTHER	PTHR24567	CRP FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN
187	235	SMART	SM00419	crpmeuga4
187	235	InterPro	IPR012318	Crp-type HTH domain
193	224	Pfam	PF00325	Bacterial regulatory proteins, crp family
193	224	InterPro	IPR012318	Crp-type HTH domain
23	162	SUPERFAMILY	SSF51206	cAMP-binding domain-like
23	162	InterPro	IPR018490	Cyclic nucleotide-binding domain superfamily
30	104	ProSiteProfiles	PS50042	cAMP/cGMP binding motif profile.
30	104	InterPro	IPR000595	Cyclic nucleotide-binding domain
195	218	ProSitePatterns	PS00042	Crp-type HTH domain signature.
195	218	InterPro	IPR018335	Transcription regulator HTH, Crp-type, conserved site
19	164	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
19	164	InterPro	IPR014710	RmlC-like jelly roll fold
166	233	CDD	cd00092	HTH_CRP
19	164	FunFam	G3DSA:2.60.120.10:FF:000004	Fumarate/nitrate reduction transcriptional regulator Fnr
164	237	ProSiteProfiles	PS51063	Crp-type HTH domain profile.
164	237	InterPro	IPR012318	Crp-type HTH domain
165	245	FunFam	G3DSA:1.10.10.10:FF:000028	Fumarate/nitrate reduction transcriptional regulator Fnr
165	244	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
165	244	InterPro	IPR036390	Winged helix DNA-binding domain superfamily

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_A0A0H3GMU3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05031	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
9				0.361
11				0.356
2				0.006
17				0.002

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	27.52	0.882
2	5.55	0.22
3	3.37	0.095
4	1.3	0.012

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
14				0.235

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	7.2	0.375
2	6.72	0.342
3	2.66	0.078
4	2.24	0.055
5	1.6	0.025

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.

56 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
2FT	3LA3	P0A4U6	168.1 Da LogP 0.57 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(C(=O)O)(F)F)C(=O)O`
AKG	3LA2	P0A4U6	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
BTB	2XGX	P29283	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
FES	5CVR	Q70ET4	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
PCG	4N9I	C3SQJ7	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)…`
SP1	4R8H	P0ACJ8	345.3 Da LogP -0.70 TPSA 137.8	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…`

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
ZINC12501894	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…`
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC33494013	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…`
ZINC4095501	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…`
ZINC88465990	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[C@H]…`
ZINC4095503	0.746	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O…`
ZINC4533542	0.746	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC4533545	0.746	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC13515981	0.701	415.3 Da LogP -0.37 TPSA 177.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O…`
ZINC25757995	0.689	346.2 Da LogP -1.81 TPSA 168.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)c2ncn([C@H]3O[C@H]4CO[P@](=O)(O)O[…`
ZINC25757999	0.689	346.2 Da LogP -1.81 TPSA 168.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)c2ncn([C@H]3O[C@H]4CO[P@@](=O)(O)O…`
ZINC12502230	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC3581269	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC3869448	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869449	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3869450	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869451	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3873977	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC4245698	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC5080458	0.656	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[…`
ZINC5080460	0.656	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)…`
ZINC5080462	0.656	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[…`
ZINC5080463	0.656	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)…`
ZINC38580931	0.651	345.2 Da LogP -1.58 TPSA 168.9	✓ Ro5	✓ Clean	`Nc1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C@…`
ZINC25757988	0.641	346.2 Da LogP -1.40 TPSA 169.0	✓ Ro5	✓ Clean	`O=c1nc(O)[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@@](=O)(O…`
ZINC25757992	0.641	346.2 Da LogP -1.40 TPSA 169.0	✓ Ro5	✓ Clean	`O=c1nc(O)[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@@](=O)(O…`
ZINC38581024	0.641	346.2 Da LogP -1.40 TPSA 169.0	✓ Ro5	✓ Clean	`O=c1nc(O)[nH]c2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(…`
ZINC38580933	0.635	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncc2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[…`
ZINC101148330	0.634	445.3 Da LogP 0.81 TPSA 153.2	✓ Ro5	✓ Clean	`O=c1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C…`
ZINC17142115	0.613	320.2 Da LogP -1.66 TPSA 172.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…`
ZINC22047759	0.613	320.2 Da LogP -1.66 TPSA 172.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…`
ZINC255997527	0.613	320.2 Da LogP -1.66 TPSA 172.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…`
ZINC33650193	0.613	320.2 Da LogP -1.66 TPSA 172.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H]3CO[P@](=O)(O)O[C@H]3[…`
ZINC33650194	0.613	320.2 Da LogP -1.66 TPSA 172.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…`
ZINC25757703	0.609	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1nc[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC25757707	0.609	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1nc[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC13516347	0.600	353.2 Da LogP -0.15 TPSA 133.2	✓ Ro5	✓ Clean	`O=[P@]1(O)OC[C@H]2O[C@@H](n3cnc4c3ncn3ccnc43)[C…`
ZINC38580945	0.597	443.4 Da LogP 0.11 TPSA 192.9	1 viol.	✓ Clean	`NCCCCCCNc1nc(N)c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(…`
ZINC4095499	0.571	305.2 Da LogP -1.40 TPSA 146.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3[C@H]…`
ZINC13516498	0.563	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC14948944	0.563	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC256769854	0.563	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC256769855	0.563	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC13829346	0.548	433.3 Da LogP 0.85 TPSA 157.9	✓ Ro5	✓ Clean	`O=C(Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@@](=O)(O)…`
ZINC31474923	0.548	419.3 Da LogP 1.21 TPSA 140.8	✓ Ro5	✓ Clean	`O=[P@@]1(O)OC[C@H]2O[C@@H](n3cnc4c(NCc5ccccc5)n…`
ZINC44559643	0.548	433.3 Da LogP 0.85 TPSA 157.9	✓ Ro5	✓ Clean	`O=C(Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC4824676	0.545	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC4824677	0.545	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC4824678	0.545	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC4824679	0.545	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`

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.