Protein profile

KP13_00485

Thiol:disulfide interchange protein DsbD

Genome: KpKP13

Gene: dsbD AHE46780.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQF1

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Amino acids 598

Annotations 7

Features 53

PDB binders 1

Druggability 0.949

Overview

Basic information about this protein and its source genome.

Accession: KP13_00485
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: dsbD AHE46780.1
Status: annotated
Amino acids: 598
Structure source: AlphaFold + ColabFold

1.8.1.8

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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:0047134 Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+. 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:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.

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 (%): 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 78.4

Selected Druggability evidence

AlphaFold / UniProt 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 0.949

Structure A0A0H3GQF1

Pocket Pocket 51

P2Rank 0.358

Structure A0A0H3GQF1

Pocket Pocket 1

ColabFold model

FPocket 0.971 · Pocket 47

P2Rank 0.417 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 104 / 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.

1 EC 6 GO

Enzyme Commission (EC)

1.8.1.8

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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:0047134 Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
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:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

53 records

Show feature table

Start	End	DB	Term	Name
443	598	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
386	396	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
421	442	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
19	156	Gene3D	G3DSA:2.60.40.1250	-
19	156	InterPro	IPR036929	Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily
27	140	SUPERFAMILY	SSF74863	Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
27	140	InterPro	IPR036929	Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily
1	19	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	19	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
202	229	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
241	265	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
205	410	Pfam	PF02683	Cytochrome C biogenesis protein transmembrane region
205	410	InterPro	IPR003834	Cytochrome C biogenesis protein, transmembrane domain
266	276	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
277	299	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
357	379	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
19	154	FunFam	G3DSA:2.60.40.1250:FF:000001	Thiol:disulfide interchange protein DsbD
389	411	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
416	420	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
480	594	SUPERFAMILY	SSF52833	Thioredoxin-like
480	594	InterPro	IPR036249	Thioredoxin-like superfamily
1	19	Phobius	SIGNAL_PEPTIDE	Signal peptide region
363	385	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
472	597	Gene3D	G3DSA:3.40.30.10	Glutaredoxin
147	180	MobiDBLite	mobidb-lite	consensus disorder prediction
397	415	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
505	523	ProSitePatterns	PS00194	Thioredoxin family active site.
505	523	InterPro	IPR017937	Thioredoxin, conserved site
4	595	PANTHER	PTHR32234	THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD
161	180	MobiDBLite	mobidb-lite	consensus disorder prediction
489	594	CDD	cd02953	DsbDgamma
489	594	InterPro	IPR035671	DsbD gamma
14	19	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
20	201	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
459	598	ProSiteProfiles	PS51352	Thioredoxin domain profile.
459	598	InterPro	IPR013766	Thioredoxin domain
322	351	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
328	350	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
472	597	FunFam	G3DSA:3.40.30.10:FF:000116	Thiol:disulfide interchange protein DsbD
1	597	Hamap	MF_00399	Thiol:disulfide interchange protein DsbD [dsbD].
1	597	InterPro	IPR022910	Thiol:disulphide interchange protein DsbD
5	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
201	223	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
277	301	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
302	321	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
424	446	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
495	570	Pfam	PF13899	Thioredoxin-like
352	362	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
243	265	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
29	138	Pfam	PF11412	Disulphide bond corrector protein DsbC
29	138	InterPro	IPR028250	Thiol:disulfide interchange protein DsbD, N-terminal domain
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
230	240	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GQF1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00485	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
51				0.949
37				0.502
39				0.241

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	5.72	0.277
2	4.45	0.189
3	2.72	0.081
4	2.61	0.076
5	1.48	0.02

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
47				0.971
41				0.366

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	6.01	0.296
2	5.76	0.28
3	2.91	0.093
4	1.63	0.026
5	1.47	0.02

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.