Protein profile

VK055_0488

pentaerythritol tetranitrate reductase

Genome: KpATCC43816

Gene: AIK79111.1 onr Structure source: Experimental + ColabFold UniProt A0A0H3GQS4

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Amino acids 365

Annotations 4

Features 9

PDB binders 20

Druggability 0.915

Overview

Basic information about this protein and its source genome.

Accession: VK055_0488
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79111.1 onr
Status: annotated
Amino acids: 365
Structure source: Experimental + ColabFold

GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016628 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.

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 (%): 37.681
Localization: Cytoplasmic
ColabFold pLDDT: 97.85

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 0.915

Structure 7TMB

Pocket Pocket 3

P2Rank 0.868

Structure 7TMB

Pocket Pocket 1

ColabFold model

FPocket 0.491 · Pocket 4

P2Rank 0.9 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 105 / 4744 genomes with a hit

Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0016628 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
5	345	CDD	cd02933	OYE_like_FMN
4	364	PANTHER	PTHR22893	NADH OXIDOREDUCTASE-RELATED
4	364	InterPro	IPR045247	Oxidoreductase Oye-like
3	365	Gene3D	G3DSA:3.20.20.70	Aldolase class I
3	365	InterPro	IPR013785	Aldolase-type TIM barrel
3	365	FunFam	G3DSA:3.20.20.70:FF:000059	N-ethylmaleimide reductase, FMN-linked
5	344	Pfam	PF00724	NADH:flavin oxidoreductase / NADH oxidase family
5	344	InterPro	IPR001155	NADH:flavin oxidoreductase/NADH oxidase, N-terminal
4	364	SUPERFAMILY	SSF51395	FMN-linked oxidoreductases

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

1 + 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 7TMB	X-ray	2.10 Å	A,B,C,D,E,F	100.0% 1-365	PDBe RCSB PDBj File	Viewing
ColabFold VK055_0488	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
36				0.912
81				0.384
21				0.283
54				0.238

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	26.97	0.918
2	25.26	0.905
3	24.83	0.901
4	23.47	0.889
5	22.34	0.88

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
4				0.491
1				0.283

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				20.08	0.849
2				1.62	0.026

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.

70 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
1L5	4JIQ	O31246	163.2 Da LogP 2.32 TPSA 43.1	✓ Ro5	✓ Clean	`C/C(=C\N(=O)=O)/c1ccccc1`
8OZ	5N6G	O31246	148.2 Da LogP 1.78 TPSA 37.3	✓ Ro5	✓ Clean	`C=C(c1ccccc1)C(=O)O`
A2Q	1GVQ	P71278	96.1 Da LogP 1.30 TPSA 17.1	✓ Ro5	✓ Clean	`C1CC=CC(=O)C1`
ANB	1H62	P71278	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@H]([C@@H]1CCC2=O)CCC4=CC(=O)C…`
BEN	6S32	K9TVC9	120.2 Da LogP 0.97 TPSA 49.9	✓ Ro5	✓ Clean	`[H]/N=C(\c1ccccc1)/N`
DNF	1GVO	P71278	184.1 Da LogP 1.21 TPSA 106.5	✓ Ro5	✓ Clean	`c1cc(c(cc1[N+](=O)[O-])[N+](=O)[O-])O`
FNR	5LGZ	P71278	458.4 Da LogP -0.93 TPSA 208.4	1 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
HBA	4JIP	O31246	122.1 Da LogP 1.20 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(ccc1C=O)O`
KSW	6S23	M2XAQ9	94.1 Da LogP 1.07 TPSA 17.1	✓ Ro5	✓ Clean	`CC1=CC=CC1=O`
NYH	3F03	P71278	127.1 Da LogP 1.72 TPSA 43.1	✓ Ro5	✓ Clean	`C1CCC(=CC1)[N+](=O)[O-]`
P7Y	3P7Y	P71278	165.1 Da LogP 1.64 TPSA 63.4	✓ Ro5	✓ Clean	`c1ccc(c(c1)/C=C/[N+](=O)[O-])O`
P80	3P80	P71278	165.1 Da LogP 1.64 TPSA 63.4	✓ Ro5	✓ Clean	`c1cc(cc(c1)O)/C=C/[N+](=O)[O-]`
P81	3P81	P71278	165.1 Da LogP 1.64 TPSA 63.4	✓ Ro5	✓ Clean	`c1cc(ccc1/C=C/[N+](=O)[O-])O`
PDN	1H61	P71278	358.4 Da LogP 3.16 TPSA 94.8	✓ Ro5	✓ Clean	`C[C@]12CC(=O)[C@H]3[C@H]([C@@H]1CC[C@@]2(C(=CO)…`
STR	1H60	P71278	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=…`
TNF	1GVS	P71278	229.1 Da LogP 1.12 TPSA 149.7	✓ Ro5	✓ Clean	`c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=O)…`
TNL	1GVR	P71278	227.1 Da LogP 1.72 TPSA 129.4	✓ Ro5	✓ Clean	`Cc1c(cc(cc1[N+](=O)[O-])[N+](=O)[O-])[N+](=O)[O…`
TXD	2R14	Q51990	667.5 Da LogP -3.30 TPSA 317.6	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
U5N	7BN6	M2XAQ9	98.1 Da LogP 0.49 TPSA 26.3	✓ Ro5	✓ Clean	`C[C@@H]1C=CC(=O)O1`
U6W	7BO0	M2XAQ9	98.1 Da LogP 0.84 TPSA 26.3	✓ Ro5	✓ Clean	`CC1=CCC(=O)O1`

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
ZINC13521486	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC13542968	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@@]4(…`
ZINC14880028	1.000	227.1 Da LogP 1.72 TPSA 129.4	✓ Ro5	✓ Clean	`Cc1c([N+](=O)[O-])cc([N+](=O)[O-])cc1[N+](=O)[O…`
ZINC156796	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)C…`
ZINC1683141	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC1883067	1.000	229.1 Da LogP 1.12 TPSA 149.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc([N+](=O)[O-])c(O)c([N+](=O)[O-…`
ZINC2100022	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)C…`
ZINC2159863	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@@H]2[C@@H]3CCC4=CC(=O)CC[C@]4…`
ZINC238924247	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4(C…`
ZINC242548813	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@H]1[C@H]2CC[C@]2(C)C(=O…`
ZINC242648889	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC253502176	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@]43C)[C@…`
ZINC3132721	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4(C…`
ZINC3874744	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@@]4…`
ZINC3881421	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@]2(C)C(…`
ZINC4023563	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43C)[…`
ZINC4023564	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@H]2CC[C@]2(C)C(=…`
ZINC4023565	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@]2(C)C(…`
ZINC4081602	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C…`
ZINC4081603	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC4428529	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C…`
ZINC4534007	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@@]12C=CC(=O)C=C1CC[C@H]1[C@H]2CC[C@@]2(C)C(…`
ZINC5260762	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@@]4…`
ZINC58482279	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@H]1[C@H]2CC[C@@]2(C)C(=…`
ZINC675050365	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@H]2[C@H]3CCC4=CC(=O)CC[C@]4(C…`
ZINC8580672	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC9212411	1.000	314.5 Da LogP 4.72 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@H]2[C@H]3CCC4=CC(=O)CC[C@]4(C)…`
ZINC69592773	0.843	344.4 Da LogP 2.29 TPSA 91.7	✓ Ro5	✓ Clean	`C[C@]12CC(=O)[C@H]3[C@H](CCC4=CC(=O)C=C[C@@]43C…`
ZINC69592779	0.843	344.4 Da LogP 2.29 TPSA 91.7	✓ Ro5	✓ Clean	`C[C@]12CC(=O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43…`
ZINC1857666496	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@@]43C)[C@…`
ZINC245224552	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)CC[C@@]43C)[C@…`
ZINC253618173	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CCC(=O)C=C1CC[C@H]1[C@H]2CC[C@@]2(C)[C@H…`
ZINC253618174	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@@]12CCC(=O)C=C1CC[C@H]1[C@H]2CC[C@]2(C)[C@H…`
ZINC253648944	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@@]43C)[C@…`
ZINC32911458	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@@]43C)[C@…`
ZINC3927796	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@@]43C)[C@…`
ZINC44830435	0.826	316.4 Da LogP 4.22 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@@]12CCC(=O)C=C1CC[C@H]1[C@H]2CC[C@@]2(C)[C@…`
ZINC4706032	0.826	300.4 Da LogP 4.33 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@H]2[C@H]3CCC4=CC(=O)C[C@@]4(C…`
ZINC4706033	0.826	300.4 Da LogP 4.33 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@H]2[C@H]3CCC4=CC(=O)C[C@@]4(C)…`
ZINC4706034	0.826	300.4 Da LogP 4.33 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)C[C@@]4(…`
ZINC4706035	0.826	300.4 Da LogP 4.33 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)[C@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)C[C@@]4(C…`
ZINC1857667003	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4…`
ZINC2170217	0.792	200.1 Da LogP 0.91 TPSA 126.7	✓ Ro5	Alert	`O=[N+]([O-])c1cc(O)c(O)c([N+](=O)[O-])c1`
ZINC21991584	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC244882669	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4…`
ZINC253498633	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@@]…`
ZINC253618167	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@H]1CC[C@@H]2[C@@H]3CCC4=CC(=O)CC[C@]4…`
ZINC253618168	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@H]1CC[C@@H]2[C@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC3927798	0.792	330.5 Da LogP 4.31 TPSA 43.4	✓ Ro5	✓ Clean	`COC(=O)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(…`
ZINC68564159	0.792	366.2 Da LogP 2.40 TPSA 213.0	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(-c2cc([N+](=O)[O-])cc([N+](=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.