Protein profile

PA0509

cytochrome C

Genome: NC_002516.2

Gene: nirN PA0509 Structure source: Experimental + AlphaFold UniProt Q9I609

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Amino acids 493

Annotations 7

Features 21

PDB binders 8

Druggability 0.527

Overview

Basic information about this protein and its source genome.

Accession: PA0509
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: nirN PA0509
Status: annotated
Amino acids: 493
Structure source: Experimental + AlphaFold

1.3.-.-

GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways. 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: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:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Unknown

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 0.527

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1.3.-.-

Gene Ontology (GO)

GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
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: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:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
1	18	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
131	484	PANTHER	PTHR47197	PROTEIN NIRF
13	98	Gene3D	G3DSA:1.10.760.10	-
13	98	InterPro	IPR036909	Cytochrome c-like domain superfamily
7	111	SUPERFAMILY	SSF46626	Cytochrome c
7	111	InterPro	IPR036909	Cytochrome c-like domain superfamily
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
129	484	Pfam	PF02239	Cytochrome D1 heme domain
3	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
19	493	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
21	92	Pfam	PF13442	Cytochrome C oxidase, cbb3-type, subunit III
21	92	InterPro	IPR009056	Cytochrome c-like domain
18	96	ProSiteProfiles	PS51007	Cytochrome c family profile.
18	96	InterPro	IPR009056	Cytochrome c-like domain
102	485	SUPERFAMILY	SSF51004	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
102	485	InterPro	IPR011048	Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
100	486	FunFam	G3DSA:2.140.10.20:FF:000002	Probable c-type cytochrome
100	486	Gene3D	G3DSA:2.140.10.20	-
100	486	InterPro	IPR003143	Cytochrome cd1-nitrite reductase, C-terminal 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

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 6RTE	X-ray	1.94 Å	A,B	95.9% 21-493	PDBe RCSB PDBj File	Viewing
PDB 6RTD	X-ray	2.36 Å	A,B	95.9% 21-493	PDBe RCSB PDBj File	Loaded
AlphaFold PA0509	AlphaFold	—	—	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				0.374

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	23.01	0.885
2	15.84	0.763
3	6.27	0.314
4	4.28	0.176
5	1.87	0.037

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
2				0.581
1				0.313

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.

58 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
BU3	6RTD 2.36 Å Open crystal	90.1 Da LogP -0.25 TPSA 40.5	✓ Ro5	✓ Clean	`C[C@H]([C@@H](C)O)O`

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
10M	5GUW	P24474	498.6 Da LogP -0.52 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCCS[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C…`
2NO	1AOM	P72181	46.0 Da LogP 0.10 TPSA 49.3	✓ Ro5	✓ Clean	`N(=O)[O]`
CMO	1DY7	P72181	28.0 Da LogP -0.04 TPSA 19.9	✓ Ro5	✓ Clean	`[C-]#[O+]`
NHE	1H9X	P72181	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
O	5GUW	P24474	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
OXY	1HJ3	P72181	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
SO2	1AOF	P72181	64.1 Da LogP -0.67 TPSA 34.1	✓ Ro5	✓ Clean	`O=S=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
ZINC100053481	1.000	484.6 Da LogP -0.91 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H…`
ZINC100057932	1.000	498.6 Da LogP -0.52 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@…`
ZINC100058001	1.000	470.6 Da LogP -1.30 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](…`
ZINC100796989	1.000	484.6 Da LogP -0.91 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC14114498	1.000	498.6 Da LogP -0.52 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC100056955	0.732	322.5 Da LogP 1.27 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC100056957	0.732	336.5 Da LogP 1.66 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C…`
ZINC100759478	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@@H…`
ZINC101659921	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]…`
ZINC16052385	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]…`
ZINC6845558	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC76945567	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@…`
ZINC77293255	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC77293258	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C@@…`
ZINC77293261	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H…`
ZINC85479681	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]…`
ZINC97943321	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@H…`
ZINC100053689	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC100053691	0.696	496.6 Da LogP -0.84 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC1501015302	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC2039285652	0.696	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285653	0.696	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285654	0.696	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285655	0.696	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2053493146	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493147	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493148	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493149	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC238809244	0.696	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C…`
ZINC238809245	0.696	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C…`
ZINC252695223	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695224	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695225	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695226	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC58649715	0.696	496.6 Da LogP -0.84 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC59978443	0.696	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](…`
ZINC66157001	0.696	468.5 Da LogP -1.62 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC70669940	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669941	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669942	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669943	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC77311968	0.696	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H]…`
ZINC83433913	0.696	426.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO…`
ZINC85482724	0.696	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC86002923	0.696	426.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCO[C@@H]1O[C@H](CO)[C@H](O[C@H]2O[C@H](CO)…`
ZINC2382416918	0.619	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O[C…`
ZINC257362199	0.619	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[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.