Protein profile

KP13_00213

Glycerol-3-phosphate dehydrogenase [NAD(P)+]

Genome: KpKP13

Gene: gpsA AHE42126.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUQ5

Export view

Amino acids 339

Annotations 14

Features 32

PDB binders 12

Druggability 0.971

Overview

Basic information about this protein and its source genome.

Accession: KP13_00213
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: gpsA AHE42126.1
Status: annotated
Amino acids: 339
Structure source: AlphaFold + ColabFold

1.1.1.94

GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP. GO:0047952 Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+. GO:0046168 The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 32.967
Human E-value: 1.6e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 92.625
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.33

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 0.971

Structure A0A0H3GUQ5

Pocket Pocket 1

P2Rank 0.92

Structure A0A0H3GUQ5

Pocket Pocket 1

ColabFold model

FPocket 0.706 · Pocket 4

P2Rank 0.951 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 164 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1.1.1.94

Gene Ontology (GO)

GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
GO:0047952 Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+.
GO:0046168 The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
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:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0141152 Catalysis of the reaction: NAD+ + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H+ + NADH.
GO:0141153 NADP+ + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H+ + NADPH.
GO:0046167 The chemical reactions and pathways resulting in the formation of glycerol-3-phosphate, a phosphoric monoester of glycerol.
GO:0046474 The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records

Show feature table

Start	End	DB	Term	Name
193	337	FunFam	G3DSA:1.10.1040.10:FF:000001	Glycerol-3-phosphate dehydrogenase [NAD(P)+]
1	191	FunFam	G3DSA:3.40.50.720:FF:000019	Glycerol-3-phosphate dehydrogenase [NAD(P)+]
184	322	Pfam	PF07479	NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
184	322	InterPro	IPR006109	Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal
6	326	Hamap	MF_00394	Glycerol-3-phosphate dehydrogenase [NAD(P)+] [gpsA].
6	326	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
2	191	Gene3D	G3DSA:3.40.50.720	-
8	182	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
8	182	InterPro	IPR036291	NAD(P)-binding domain superfamily
60	87	PRINTS	PR00077	NAD-dependent glycerol-3-phosphate dehydrogenase signature
60	87	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
177	201	PRINTS	PR00077	NAD-dependent glycerol-3-phosphate dehydrogenase signature
177	201	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
136	156	PRINTS	PR00077	NAD-dependent glycerol-3-phosphate dehydrogenase signature
136	156	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
202	226	PRINTS	PR00077	NAD-dependent glycerol-3-phosphate dehydrogenase signature
202	226	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
10	27	PRINTS	PR00077	NAD-dependent glycerol-3-phosphate dehydrogenase signature
10	27	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
242	259	PRINTS	PR00077	NAD-dependent glycerol-3-phosphate dehydrogenase signature
242	259	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
7	323	PANTHER	PTHR11728	GLYCEROL-3-PHOSPHATE DEHYDROGENASE
192	213	ProSitePatterns	PS00957	NAD-dependent glycerol-3-phosphate dehydrogenase signature.
192	213	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
1	336	PIRSF	PIRSF000114	Glycerol-3-P_dh
1	336	InterPro	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent
193	339	Gene3D	G3DSA:1.10.1040.10	-
193	339	InterPro	IPR013328	6-phosphogluconate dehydrogenase, domain 2
8	163	Pfam	PF01210	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
8	163	InterPro	IPR011128	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal
184	335	SUPERFAMILY	SSF48179	6-phosphogluconate dehydrogenase C-terminal domain-like
184	335	InterPro	IPR008927	6-phosphogluconate dehydrogenase-like, 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...

Legend High Medium Low

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_A0A0H3GUQ5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00213	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				0.971

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	19.84	0.846
2	6.36	0.32
3	2.25	0.056

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
4				0.706

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	24.73	0.901
2	7.37	0.385
3	1.53	0.022

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.

62 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
13P	1WPQ	P21695	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C(C(=O)COP(=O)(O)O)O`
3SY	6E8Y	P21695	136.1 Da LogP -2.06 TPSA 80.9	✓ Ro5	✓ Clean	`C(C(CO)(CO)CO)O`
BCP	1M66	P90551	233.5 Da LogP 1.77 TPSA 54.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)nc(nc2Cl)Br`
BOA	1M67	P90551	215.0 Da LogP 0.82 TPSA 74.7	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)nc(nc2O)Br`
CFP	1JDJ	P90551	172.6 Da LogP 1.15 TPSA 54.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(nc(n2)F)Cl`
G3H	1Z82	A0A0F6AK91	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C([C@H](C=O)O)OP(=O)(O)O`
G3P	1Z82	A0A0F6AK91	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C([C@H](COP(=O)(O)O)O)O`
MYS	1JDJ	P90551	212.4 Da LogP 6.10 TPSA 0.0	1 viol.	✓ Clean	`CCCCCCCCCCCCCCC`
NDE	1N1E	P90551	831.5 Da LogP -4.94 TPSA 425.2	3 viol.	✓ Clean	`c1c[n+](cc(c1[C@H](C(=O)COP(=O)(O)O)O)C(=O)N)[C…`
NH4	1TXG	O29390	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
PLM	1M66	P90551	256.4 Da LogP 5.55 TPSA 37.3	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)O`
POP	6PYP	P21695	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[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
ZINC1529498	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC15752737	1.000	233.5 Da LogP 1.77 TPSA 54.5	✓ Ro5	✓ Clean	`Clc1nc(Br)nc2nc[nH]c12`
ZINC1628119	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC138457918	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC3160730	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC2378801	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC2113934081	0.762	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668	0.762	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.762	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.762	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC1529620	0.739	246.2 Da LogP -2.17 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(OC[C@@H](O)CO)OC[C@@H](O)CO`
ZINC2387442	0.739	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC31778284	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C\C(=O)CCCCCCCC(=O)O`
ZINC5540108	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C/C(=O)CCCCCCCC(=O)O`
ZINC64633397	0.739	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC59545317	0.727	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCC(=O)O`
ZINC59545320	0.727	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)CCC(=O)O`
ZINC59545336	0.727	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCC(=O)O`
ZINC100292624	0.708	344.4 Da LogP 2.63 TPSA 111.9	✓ Ro5	✓ Clean	`CCCCCCC(=O)[C@@H](O)[C@H](O)C(=O)CCCCCCCC(=O)O`
ZINC136729993	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@@H](O)CCCCCCCC(=O)O`
ZINC14502373	0.708	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CCCCCCCC(=O)O`
ZINC1600678	0.708	264.4 Da LogP 2.63 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCS(=O)(=O)CCCCC(=O)O`
ZINC30726317	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)[C@H](O)CCCCCCCC(=O)O`
ZINC30730192	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCC[C@H](O)[C@@H](O)CCCCCCCC(=O)O`
ZINC33820346	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)[C@@H](O)CCCCCCCCCCC(=O)O`
ZINC59200967	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCCCCC(=O)O`
ZINC59206873	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCC[C@H](O)[C@H](O)CCCCCCCC(=O)O`
ZINC59724711	0.708	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCCC(=O)O`
ZINC8220964	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)[C@@H](O)CCCCCCCC(=O)O`
ZINC85857782	0.708	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](O)CCCCCCC(=O)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.