Protein profile

VK055_1891

dimethyl sulfoxide reductase, chain A

Genome: KpATCC43816

Gene: AIK80497.1 dmsA3 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLB2

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Amino acids 769

Annotations 6

Features 17

PDB binders 13

Druggability 0.997

Overview

Basic information about this protein and its source genome.

Accession: VK055_1891
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80497.1 dmsA3
Status: annotated
Amino acids: 769
Structure source: AlphaFold + ColabFold

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:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands. GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. 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:0030151 Binding to a molybdenum ion (Mo). GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.

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 (%): 32.219
Localization: Periplasmic
ColabFold pLDDT: 96.55

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 0.997

Structure A0A0H3GLB2

Pocket Pocket 1

P2Rank 0.995

Structure A0A0H3GLB2

Pocket Pocket 1

ColabFold model

FPocket 0.996 · Pocket 1

P2Rank 0.988 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 13 / 4744 genomes with a hit

Normalized 0.003

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

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:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
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:0030151 Binding to a molybdenum ion (Mo).
GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
11	625	SUPERFAMILY	SSF53706	Formate dehydrogenase/DMSO reductase, domains 1-3
622	749	CDD	cd02793	MopB_CT_DMSOR-BSOR-TMAOR
622	749	InterPro	IPR041954	Trimethylamine-N-oxide reductase-like, molybdopterin-binding domain
52	507	Pfam	PF00384	Molybdopterin oxidoreductase
52	507	InterPro	IPR006656	Molybdopterin oxidoreductase
598	761	Gene3D	G3DSA:2.40.40.20	-
144	590	Gene3D	G3DSA:3.40.228.10	Dimethylsulfoxide Reductase, domain 2
10	750	PANTHER	PTHR43742	TRIMETHYLAMINE-N-OXIDE REDUCTASE
624	744	Pfam	PF01568	Molydopterin dinucleotide binding domain
624	744	InterPro	IPR006657	Molybdopterin dinucleotide-binding domain
11	47	Pfam	PF18364	Molybdopterin oxidoreductase N-terminal domain
11	47	InterPro	IPR041460	Molybdopterin oxidoreductase, N-terminal
46	557	Gene3D	G3DSA:3.90.55.10	Dimethylsulfoxide Reductase, domain 3
52	516	Gene3D	G3DSA:3.40.50.740	-
709	733	MobiDBLite	mobidb-lite	consensus disorder prediction
619	768	SUPERFAMILY	SSF50692	ADC-like
619	768	InterPro	IPR009010	Aspartate decarboxylase-like 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

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_A0A0H3GLB2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1891	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
1				0.997
3				0.887
39				0.838
2				0.457

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	42.74	0.968
2	4.86	0.217
3	3.07	0.102
4	3.03	0.1
5	2.63	0.077

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				0.996
2				0.978

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	30.87	0.936
2	7.94	0.422
3	7.01	0.363
4	5.02	0.228
5	3.83	0.149

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.

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
2MD	1TMO	O87948	742.6 Da LogP -2.53 TPSA 346.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
2MO	1E61	Q52675	127.9 Da LogP -0.24 TPSA 34.1	✓ Ro5	✓ Clean	`O=[Mo]=O`
4MO	2DMR	Q52675	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+4]`
6MO	1DMR	Q52675	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+6]`
6WO	1E18	Q52675	199.8 Da LogP -0.12 TPSA 17.1	✓ Ro5	✓ Clean	`O=[W+4]`
BTT	4V4E	P80563	142.1 Da LogP 0.51 TPSA 80.9	✓ Ro5	Alert	`c1c(c(cc(c1O)O)O)O`
MGD	4V4C	P80563	740.6 Da LogP -2.06 TPSA 346.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
NO2	1FDI	P07658	46.0 Da LogP 0.25 TPSA 52.5	✓ Ro5	✓ Clean	`N(=O)[O-]`
O	1DMR	Q52675	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
PGD	1DMR	Q52675	738.6 Da LogP -2.97 TPSA 343.0	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
PYG	4V4D	P80563	126.1 Da LogP 0.80 TPSA 60.7	✓ Ro5	Alert	`c1cc(c(c(c1)O)O)O`
SO2	2DMR	Q52675	64.1 Da LogP -0.67 TPSA 34.1	✓ Ro5	✓ Clean	`O=S=O`
W	2E7Z	Q71EW5	183.8 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[W+6]`

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
ZINC12504289	0.689	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC6091722	0.667	218.2 Da LogP 2.18 TPSA 80.9	✓ Ro5	Alert	`Oc1cccc(-c2cccc(O)c2O)c1O`
ZINC104869865	0.642	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC34541308	0.642	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.642	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.642	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.642	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.642	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC38229869	0.636	324.3 Da LogP 3.38 TPSA 121.4	1 viol.	Alert	`Oc1cc2c3cc(O)c(O)cc3c3cc(O)c(O)cc3c2cc1O`
ZINC59636950	0.588	236.0 Da LogP 1.70 TPSA 40.5	✓ Ro5	Alert	`Oc1cccc(I)c1O`
ZINC12501413	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	0.573	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC13377064	0.571	218.2 Da LogP 2.18 TPSA 80.9	✓ Ro5	✓ Clean	`Oc1cccc(O)c1-c1c(O)cccc1O`
ZINC254871	0.538	267.9 Da LogP 2.62 TPSA 40.5	✓ Ro5	Alert	`Oc1cc(Br)c(Br)cc1O`
ZINC17375772	0.535	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@@H]3O[C@@H](CO[P@](=O)(O)OP(=O…`
ZINC8618621	0.535	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8618622	0.535	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8618623	0.535	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC106686432	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP…`
ZINC12958393	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)O…`
ZINC35024781	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…`
ZINC35024785	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…`
ZINC35024786	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)…`
ZINC4261903	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O…`
ZINC80601236	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O…`
ZINC95921560	0.529	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…`
ZINC100058967	0.517	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@H](CO[P@](=O)(O)OP(=O)…`
ZINC12504287	0.517	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC12504288	0.517	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC31308647	0.517	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC71774763	0.516	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC12503703	0.506	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…`
ZINC8215878	0.506	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…`
ZINC1713871	0.500	267.9 Da LogP 2.62 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)c(Br)cc1Br`
ZINC221342725	0.500	350.3 Da LogP 2.91 TPSA 121.4	1 viol.	Alert	`Oc1cc2c(cc1O)C1c3cc(O)c(O)cc3C2c2cc(O)c(O)cc21`
ZINC32257174	0.500	236.0 Da LogP 1.70 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cccc(O)c1I`
ZINC3843434	0.500	280.3 Da LogP 3.12 TPSA 80.9	✓ Ro5	Alert	`Oc1cc2c(cc1O)Sc1cc(O)c(O)cc1S2`
ZINC4262226	0.500	366.4 Da LogP 3.01 TPSA 121.4	1 viol.	Alert	`Oc1cc2c(cc1O)Cc1cc(O)c(O)cc1Cc1cc(O)c(O)cc1C2`

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.