Protein profile

PA2478

thiol:disulfide interchange protein DsbD

Genome: NC_002516.2

Gene: PA2478 dsbD2 Structure source: AlphaFold UniProt Q9I104

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Amino acids 587

Annotations 8

Features 52

PDB binders 1

Druggability 0.952

Overview

Basic information about this protein and its source genome.

Accession: PA2478
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2478 dsbD2
Status: annotated
Amino acids: 587
Structure source: AlphaFold

1.8.1.8

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. 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:0047134 Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+. GO:0015035 Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds. GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell. GO:0017004 The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.

Target profile

Computed evidence for target prioritization.

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

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 0.952

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1.8.1.8

Gene Ontology (GO)

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
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:0047134 Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
GO:0015035 Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.
GO:0017004 The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

52 records

Show feature table

Start	End	DB	Term	Name
289	311	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
448	585	ProSiteProfiles	PS51352	Thioredoxin domain profile.
448	585	InterPro	IPR013766	Thioredoxin domain
407	417	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
459	586	Gene3D	G3DSA:3.40.30.10	Glutaredoxin
1	584	Hamap	MF_00399	Thiol:disulfide interchange protein DsbD [dsbD].
1	584	InterPro	IPR022910	Thiol:disulphide interchange protein DsbD
3	12	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
31	141	SUPERFAMILY	SSF74863	Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
31	141	InterPro	IPR036929	Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily
177	355	Pfam	PF02683	Cytochrome C biogenesis protein transmembrane region
177	355	InterPro	IPR003834	Cytochrome C biogenesis protein, transmembrane domain
480	578	SUPERFAMILY	SSF52833	Thioredoxin-like
480	578	InterPro	IPR036249	Thioredoxin-like superfamily
32	137	Pfam	PF11412	Disulphide bond corrector protein DsbC
32	137	InterPro	IPR028250	Thiol:disulfide interchange protein DsbD, N-terminal domain
200	210	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
361	381	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
440	587	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
210	232	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
13	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	18	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
169	199	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
236	246	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
361	380	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
247	269	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
418	440	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
2	583	PANTHER	PTHR32234	THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD
19	168	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
350	360	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
382	386	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
27	150	Gene3D	G3DSA:2.60.40.1250	-
27	150	InterPro	IPR036929	Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily
478	580	CDD	cd02953	DsbDgamma
478	580	InterPro	IPR035671	DsbD gamma
290	320	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
384	406	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
181	203	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
270	289	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1	18	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
476	547	Pfam	PF13899	Thioredoxin-like
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
247	269	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
418	439	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
387	406	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
326	349	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
326	348	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
321	325	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
211	235	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
492	510	ProSitePatterns	PS00194	Thioredoxin family active site.
492	510	InterPro	IPR017937	Thioredoxin, conserved site

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 PA2478	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
1				0.952
32				0.351

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.

51 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
DTT	3PFU	P36655	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`

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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1580159	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC142610155	0.579	340.4 Da LogP -0.84 TPSA 112.9	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCOCCO`
ZINC1542984426	0.579	428.5 Da LogP -0.80 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1542984432	0.579	398.4 Da LogP -0.43 TPSA 122.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC207588231	0.579	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`CNCCOCCOCCOCCO`
ZINC258828116	0.579	452.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC258836919	0.579	364.4 Da LogP -0.27 TPSA 84.8	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC39267847	0.579	208.2 Da LogP -0.89 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCO`
ZINC575440725	0.579	295.4 Da LogP -1.03 TPSA 80.6	✓ Ro5	✓ Clean	`CN(CCOCCOCCO)CCOCCOCCO`
ZINC83254085	0.579	354.4 Da LogP -0.45 TPSA 112.9	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCO`
ZINC83254087	0.579	266.3 Da LogP -0.48 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCO`
ZINC95920522	0.579	296.3 Da LogP -0.85 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCO`
ZINC96503406	0.579	276.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCO`
ZINC96503425	0.579	222.2 Da LogP -0.50 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCO`
ZINC96503526	0.579	442.5 Da LogP -0.41 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCO`

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.