Protein profile

PA1781

assimilatory nitrite reductase large subunit

Genome: NC_002516.2

Gene: PA1781 nirB Structure source: AlphaFold UniProt Q9I2W1

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Amino acids 816

Annotations 11

Features 52

PDB binders 7

Druggability 0.383

Overview

Basic information about this protein and its source genome.

Accession: PA1781
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA1781 nirB
Status: annotated
Amino acids: 816
Structure source: AlphaFold

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: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: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:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring. GO:0046872 Binding to a metal ion. 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 (%): 31.071
Human E-value: 3.16e-25
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.383

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 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: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: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:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
GO:0046872 Binding to a metal ion.
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:0098809 Catalysis of the reaction: nitrite + acceptor = product(s) of nitrate reduction + reduced acceptor.
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: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: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.

52 records

Show feature table

Start	End	DB	Term	Name
319	385	Pfam	PF18267	Rubredoxin NAD+ reductase C-terminal domain
319	385	InterPro	IPR041575	NADH-rubredoxin oxidoreductase, C-terminal
418	470	CDD	cd19943	NirB_Fer2_BFD-like_1
571	636	Gene3D	G3DSA:3.90.480.10	Sulfite Reductase Hemoprotein;Domain 2
318	398	Gene3D	G3DSA:3.30.390.30	-
318	398	InterPro	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily
634	800	SUPERFAMILY	SSF56014	Nitrite and sulphite reductase 4Fe-4S domain-like
634	800	InterPro	IPR045854	Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
5	283	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
5	283	InterPro	IPR023753	FAD/NAD(P)-binding domain
422	474	Gene3D	G3DSA:1.10.10.1100	-
422	474	InterPro	IPR041854	BFD-like [2Fe-2S]-binding domain superfamily
488	538	Pfam	PF04324	BFD-like [2Fe-2S] binding domain
488	538	InterPro	IPR007419	BFD-like [2Fe-2S]-binding domain
423	471	Pfam	PF04324	BFD-like [2Fe-2S] binding domain
423	471	InterPro	IPR007419	BFD-like [2Fe-2S]-binding domain
486	537	CDD	cd19944	NirB_Fer2_BFD-like_2
637	805	Gene3D	G3DSA:3.30.413.10	Sulfite Reductase Hemoprotein, domain 1
637	805	InterPro	IPR045854	Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
5	27	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
274	281	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
235	249	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
147	172	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
637	655	PRINTS	PR00397	Sirohaem Fe-binding site signature
637	655	InterPro	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
680	698	PRINTS	PR00397	Sirohaem Fe-binding site signature
680	698	InterPro	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
115	241	Gene3D	G3DSA:3.50.50.60	-
115	241	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	815	PIRSF	PIRSF037149	NirB
1	815	InterPro	IPR017121	Nitrite reductase [NAD(P)H], large subunit
110	246	FunFam	G3DSA:3.50.50.60:FF:000033	Nitrite reductase [NAD(P)H], large subunit
2	807	PANTHER	PTHR43809	NITRITE REDUCTASE (NADH) LARGE SUBUNIT
6	798	NCBIfam	TIGR02374	nitrite reductase large subunit NirB
6	798	InterPro	IPR012744	Nitrite reductase [NAD(P)H] large subunit, NirB
2	306	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
2	306	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
633	772	Pfam	PF01077	Nitrite and sulphite reductase 4Fe-4S domain
633	772	InterPro	IPR006067	Nitrite/sulphite reductase 4Fe-4S domain
102	120	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
234	250	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
6	25	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
147	165	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
259	281	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
7	292	Gene3D	G3DSA:3.50.50.60	-
7	292	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
522	642	SUPERFAMILY	SSF55124	Nitrite/Sulfite reductase N-terminal domain-like
522	642	InterPro	IPR036136	Nitrite/Sulfite reductase ferredoxin-like domain superfamily
680	696	ProSitePatterns	PS00365	Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.
680	696	InterPro	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
563	625	Pfam	PF03460	Nitrite/Sulfite reductase ferredoxin-like half domain
563	625	InterPro	IPR005117	Nitrite/Sulfite reductase ferredoxin-like 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
AlphaFold PA1781	AlphaFold	—	—	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
4				0.383
1				0.34

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.