Protein profile

KP13_00962

Anaerobic glycerol-3-phosphate dehydrogenase subunit A

Genome: KpKP13

Gene: AHE43508.1 glpA Structure source: AlphaFold + ColabFold UniProt A0A0H3GW84

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Amino acids 540

Annotations 11

Features 38

PDB binders 1

Druggability 0.822

Overview

Basic information about this protein and its source genome.

Accession: KP13_00962
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43508.1 glpA
Status: annotated
Amino acids: 540
Structure source: AlphaFold + ColabFold

1.1.5.3

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:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0009331 An enzyme complex that catalyzes the oxidation of sn-glycerol 3-phosphate to dihydroxyacetone phosphate, with concurrent reduction of flavin adenine dinucleotide (FAD) to FADH2. In E. coli, the complex is either a GlpA-GlpB-GlpC heterotrimer that functions in anaerobic conditions, or a GlpD homodimer that functions in aerobic conditions. GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol. 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:0004368 Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.0
Human E-value: 5.53e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 68.431
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.3

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 0.822

Structure A0A0H3GW84

Pocket Pocket 5

P2Rank 0.975

Structure A0A0H3GW84

Pocket Pocket 1

ColabFold model

FPocket 0.677 · Pocket 1

P2Rank 0.982 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 253 / 4744 genomes with a hit

Normalized 0.053

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1.1.5.3

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:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0009331 An enzyme complex that catalyzes the oxidation of sn-glycerol 3-phosphate to dihydroxyacetone phosphate, with concurrent reduction of flavin adenine dinucleotide (FAD) to FADH2. In E. coli, the complex is either a GlpA-GlpB-GlpC heterotrimer that functions in anaerobic conditions, or a GlpD homodimer that functions in aerobic conditions.
GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
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:0004368 Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
GO:0046174 The chemical reactions and pathways resulting in the breakdown of a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms.
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:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
GO:0046168 The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records

Show feature table

Start	End	DB	Term	Name
418	491	Gene3D	G3DSA:1.10.10.1100	-
418	491	InterPro	IPR041854	BFD-like [2Fe-2S]-binding domain superfamily
12	29	ProSitePatterns	PS00977	FAD-dependent glycerol-3-phosphate dehydrogenase signature 1.
12	29	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
312	392	FunFam	G3DSA:3.50.50.60:FF:000096	Glycerol-3-phosphate dehydrogenase
8	536	NCBIfam	TIGR03377	anaerobic glycerol-3-phosphate dehydrogenase subunit GlpA
8	536	InterPro	IPR017752	Glycerol-3-phosphate dehydrogenase, GlpA subunit
8	525	PANTHER	PTHR11985	GLYCEROL-3-PHOSPHATE DEHYDROGENASE
8	525	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
2	120	FunFam	G3DSA:3.50.50.60:FF:000102	Glycerol-3-phosphate dehydrogenase
9	357	Pfam	PF01266	FAD dependent oxidoreductase
9	357	InterPro	IPR006076	FAD dependent oxidoreductase
3	117	Gene3D	G3DSA:3.50.50.60	-
3	117	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
122	248	Gene3D	G3DSA:3.50.50.60	-
122	248	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
418	490	FunFam	G3DSA:1.10.10.1100:FF:000003	Glycerol-3-phosphate dehydrogenase
298	388	Gene3D	G3DSA:3.50.50.60	-
298	388	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
80	92	PRINTS	PR01001	FAD-dependent glycerol-3-phosphate dehydrogenase family signature
80	92	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
20	30	PRINTS	PR01001	FAD-dependent glycerol-3-phosphate dehydrogenase family signature
20	30	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
36	48	PRINTS	PR01001	FAD-dependent glycerol-3-phosphate dehydrogenase family signature
36	48	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
345	357	PRINTS	PR01001	FAD-dependent glycerol-3-phosphate dehydrogenase family signature
345	357	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
7	19	PRINTS	PR01001	FAD-dependent glycerol-3-phosphate dehydrogenase family signature
7	19	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
309	315	PRINTS	PR01001	FAD-dependent glycerol-3-phosphate dehydrogenase family signature
309	315	InterPro	IPR000447	FAD-dependent glycerol-3-phosphate dehydrogenase
350	360	ProSitePatterns	PS00978	FAD-dependent glycerol-3-phosphate dehydrogenase signature 2.
430	483	CDD	cd19946	GlpA-like_Fer2_BFD-like
224	315	SUPERFAMILY	SSF54373	FAD-linked reductases, C-terminal domain
430	482	Pfam	PF04324	BFD-like [2Fe-2S] binding domain
430	482	InterPro	IPR007419	BFD-like [2Fe-2S]-binding domain
8	320	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
8	320	InterPro	IPR036188	FAD/NAD(P)-binding 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_A0A0H3GW84	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00962	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
5				0.822
1				0.36

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	33.86	0.948
2	23.61	0.89
3	2.25	0.055
4	1.2	0.011

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				0.677

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	22.38	0.88
2	20.15	0.851
3	14.75	0.733

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
THG	4PAA	Q63342	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…`

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
ZINC4228235	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…`
ZINC4228236	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…`
ZINC4228237	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…`
ZINC4228238	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…`
ZINC8618631	0.848	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H]…`
ZINC8627114	0.848	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)N[C@@H…`
ZINC4228247	0.712	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CN(C=O)c1ccc(C(=O)N[C…`
ZINC2005305	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC2572666	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…`
ZINC4228266	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC4228267	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…`
ZINC9212425	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212426	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC9212427	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212428	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC8618632	0.635	459.5 Da LogP 0.52 TPSA 211.8	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@H](CC…`
ZINC8627115	0.635	459.5 Da LogP 0.52 TPSA 211.8	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC…`
ZINC4228265	0.630	443.4 Da LogP 0.01 TPSA 211.9	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC4517559	0.630	443.4 Da LogP 0.01 TPSA 211.9	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@H](CCC(…`
ZINC8655682	0.628	487.5 Da LogP -0.34 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…`
ZINC13887836	0.616	429.4 Da LogP 0.54 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[C@@H](CCc1ccc(C(=O)N[C@@H](…`
ZINC4658141	0.608	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)C[C@H](CCc1ccc(C(=O)N[C@H](C…`
ZINC4658144	0.608	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)C[C@@H](CCc1ccc(C(=O)N[C@H](…`
ZINC4228269	0.605	456.4 Da LogP -0.61 TPSA 193.7	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…`
ZINC4228270	0.605	456.4 Da LogP -0.61 TPSA 193.7	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…`
ZINC4654270	0.592	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC4654271	0.592	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC13515262	0.589	439.4 Da LogP 1.17 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC4228243	0.584	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC4228244	0.584	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@H](CCC(=…`
ZINC4654260	0.584	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC8664075	0.580	330.3 Da LogP 0.76 TPSA 145.2	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)O)cc1)…`
ZINC77301924	0.573	443.4 Da LogP 0.07 TPSA 204.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[C@H](CCc1ccc(C(=O)N[C@H](CC…`
ZINC1567048	0.568	440.4 Da LogP 0.56 TPSA 200.4	1 viol.	✓ Clean	`Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC1995991	0.568	439.4 Da LogP 1.17 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2ccc(NCc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC4261891	0.560	441.4 Da LogP -0.04 TPSA 213.3	1 viol.	✓ Clean	`Nc1nc2nc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)c…`
ZINC17380277	0.551	469.5 Da LogP 0.39 TPSA 213.3	1 viol.	✓ Clean	`Nc1nc2ncc(CCCNc3ccc(C(=O)N[C@H](CCC(=O)O)C(=O)O…`
ZINC31350053	0.551	458.5 Da LogP 0.03 TPSA 208.8	1 viol.	✓ Clean	`CN(C[C@@H]1CNc2nc(N)nc(N)c2N1)c1ccc(C(=O)N[C@@H…`
ZINC31350056	0.551	458.5 Da LogP 0.03 TPSA 208.8	1 viol.	✓ Clean	`CN(C[C@H]1CNc2nc(N)nc(N)c2N1)c1ccc(C(=O)N[C@@H]…`
ZINC4826295	0.551	469.5 Da LogP 0.39 TPSA 213.3	1 viol.	✓ Clean	`Nc1nc2ncc(CCCNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)…`
ZINC8536462	0.550	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H](CN(C=O)c1ccc(C(=O)N[…`
ZINC8628600	0.550	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@@H]1CCNc1ccc(C(=O)N[C…`
ZINC8628601	0.550	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@…`
ZINC8642279	0.548	432.4 Da LogP 0.03 TPSA 213.5	1 viol.	✓ Clean	`Nc1nc(=O)c(CCCNc2ccc(C(=O)N[C@@H](CCC(=O)O)C(=O…`
ZINC5385736	0.547	439.4 Da LogP 1.17 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc(=O)c2cc(NCc3ccc(C(=O)N[C@H](CCC(=O)O)C(=O…`
ZINC1689613	0.539	442.5 Da LogP 0.91 TPSA 193.5	1 viol.	✓ Clean	`Nc1nc(N)c2c(n1)CC[C@H](CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC1689614	0.539	442.5 Da LogP 0.91 TPSA 193.5	1 viol.	✓ Clean	`Nc1nc(N)c2c(n1)CC[C@@H](CNc1ccc(C(=O)N[C@@H](CC…`
ZINC1689615	0.539	442.5 Da LogP 0.91 TPSA 193.5	1 viol.	✓ Clean	`Nc1nc(N)c2c(n1)CC[C@H](CNc1ccc(C(=O)N[C@H](CCC(…`
ZINC1689616	0.539	442.5 Da LogP 0.91 TPSA 193.5	1 viol.	✓ Clean	`Nc1nc(N)c2c(n1)CC[C@@H](CNc1ccc(C(=O)N[C@H](CCC…`
ZINC1605633	0.538	444.5 Da LogP -1.44 TPSA 216.5	1 viol.	✓ Clean	`NC1=NC(N)=C2N[C@@H](CNc3ccc(C(=O)N[C@@H](CCC(=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.