Protein profile

VK055_0231

nitrite reductase [NAD(P)H], small subunit

Genome: KpATCC43816

Gene: nirD AIK78859.1 Structure source: ColabFold

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Amino acids 957

Annotations 8

Features 63

PDB binders 7

Druggability 0.999

Overview

Basic information about this protein and its source genome.

Accession: VK055_0231
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: nirD AIK78859.1
Status: annotated
Amino acids: 957
Structure source: ColabFold

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. 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:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. 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. GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring. GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 26.689
Human E-value: 5.38e-17
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 33.801
Localization: Cytoplasmic
ColabFold pLDDT: 90.74

Selected Druggability evidence

ColabFold / curated 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 0.999

Structure CB_VK055_0231

Pocket Pocket 1

P2Rank 0.789

Structure CB_VK055_0231

Pocket Pocket 1

ColabFold model

FPocket 0.999 · Pocket 1

P2Rank 0.789 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 132 / 4744 genomes with a hit

Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

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.
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:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
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.
GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
GO:0008942 Catalysis of the reaction: NH4+ + 3 NAD(P)+ + 2 H2O = nitrite + 3 NAD(P)H + 5 H+.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

63 records

Show feature table

Start	End	DB	Term	Name
259	281	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
6	25	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
232	248	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
147	165	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
102	120	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
629	793	Gene3D	G3DSA:3.30.413.10	Sulfite Reductase Hemoprotein, domain 1
629	793	InterPro	IPR045854	Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
3	944	PANTHER	PTHR43809	NITRITE REDUCTASE (NADH) LARGE SUBUNIT
149	308	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
149	308	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
6	190	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
6	190	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
636	759	FunFam	G3DSA:3.30.413.10:FF:000007	Nitrite reductase [NAD(P)H] large subunit
6	799	NCBIfam	TIGR02374	nitrite reductase large subunit NirB
6	799	InterPro	IPR012744	Nitrite reductase [NAD(P)H] large subunit, NirB
421	474	Gene3D	G3DSA:1.10.10.1100	-
421	474	InterPro	IPR041854	BFD-like [2Fe-2S]-binding domain superfamily
318	396	Gene3D	G3DSA:3.30.390.30	-
318	396	InterPro	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily
421	473	FunFam	G3DSA:1.10.10.1100:FF:000002	Nitrite reductase large subunit
845	945	Pfam	PF13806	Rieske-like [2Fe-2S] domain
845	945	InterPro	IPR012748	Rieske-like [2Fe-2S] domain, NirD-type
677	693	ProSitePatterns	PS00365	Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.
677	693	InterPro	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
845	946	NCBIfam	TIGR02378	nitrite reductase small subunit NirD
845	946	InterPro	IPR012748	Rieske-like [2Fe-2S] domain, NirD-type
500	639	SUPERFAMILY	SSF55124	Nitrite/Sulfite reductase N-terminal domain-like
500	639	InterPro	IPR036136	Nitrite/Sulfite reductase ferredoxin-like domain superfamily
845	946	CDD	cd03529	Rieske_NirD
631	803	SUPERFAMILY	SSF56014	Nitrite and sulphite reductase 4Fe-4S domain-like
631	803	InterPro	IPR045854	Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
147	172	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
233	247	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
105	114	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
274	281	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
481	530	CDD	cd19944	NirB_Fer2_BFD-like_2
841	949	Gene3D	G3DSA:2.102.10.10	-
841	949	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
558	620	Pfam	PF03460	Nitrite/Sulfite reductase ferredoxin-like half domain
558	620	InterPro	IPR005117	Nitrite/Sulfite reductase ferredoxin-like domain
842	947	ProSiteProfiles	PS51300	NADH-nitrite reductase subunit D family profile.
7	281	Gene3D	G3DSA:3.50.50.60	-
7	281	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
318	387	Pfam	PF18267	Rubredoxin NAD+ reductase C-terminal domain
318	387	InterPro	IPR041575	NADH-rubredoxin oxidoreductase, C-terminal
318	399	FunFam	G3DSA:3.30.390.30:FF:000006	Nitrite reductase large subunit
630	768	Pfam	PF01077	Nitrite and sulphite reductase 4Fe-4S domain
630	768	InterPro	IPR006067	Nitrite/sulphite reductase 4Fe-4S domain
422	469	Pfam	PF04324	BFD-like [2Fe-2S] binding domain
422	469	InterPro	IPR007419	BFD-like [2Fe-2S]-binding domain
110	244	FunFam	G3DSA:3.50.50.60:FF:000033	Nitrite reductase [NAD(P)H], large subunit
845	945	ProSiteProfiles	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.
845	945	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur domain
634	652	PRINTS	PR00397	Sirohaem Fe-binding site signature
634	652	InterPro	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
677	695	PRINTS	PR00397	Sirohaem Fe-binding site signature
677	695	InterPro	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
844	947	SUPERFAMILY	SSF50022	ISP domain
844	947	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
110	244	Gene3D	G3DSA:3.50.50.60	-
110	244	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
6	288	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
6	288	InterPro	IPR023753	FAD/NAD(P)-binding domain

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold VK055_0231	ColabFold	—	—	full sequence	—	Viewing

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				0.999
51				0.436

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	11.39	0.609
2	10.97	0.588
3	8.59	0.459
4	4.88	0.219
5	3.09	0.104

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.

33 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
APR	2GR2	Q52437	559.3 Da LogP -3.28 TPSA 291.5	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
AZI	2BCP	Q5XC60	42.0 Da LogP 0.87 TPSA 58.7	✓ Ro5	Alert	`[N-]=[N+]=[N-]`
BU3	6TUK	Q47QF8	90.1 Da LogP -0.25 TPSA 40.5	✓ Ro5	✓ Clean	`C[C@H]([C@@H](C)O)O`
CA6	4EM3	Q2FIA5	841.6 Da LogP -1.77 TPSA 380.7	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`
CA8	4EM4	Q2FIA5	903.7 Da LogP -0.34 TPSA 380.7	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`
CAJ	4EMW	Q2FIA5	835.6 Da LogP -0.86 TPSA 372.9	3 viol.	✓ Clean	`CCOC(=O)CCCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](…`
OXY	5ER0	Q03Q85	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`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
ZINC12360703	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC4806433	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586022	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC12501123	0.553	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234	0.553	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662	0.553	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663	0.553	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC12360002	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586019	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC3871401	0.506	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871402	0.506	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3871403	0.506	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871404	0.506	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC4096223	0.506	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC12501218	0.500	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC12503850	0.500	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC13540909	0.500	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC141161066	0.500	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.500	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.500	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=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.