Protein profile

KP13_32247

Glyceraldehyde-3-phosphate dehydrogenase

Genome: KpKP13

Gene: AHE45073.1 gapA Structure source: AlphaFold + ColabFold UniProt A0A0H3GN34

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Amino acids 331

Annotations 7

Features 31

PDB binders 8

Druggability 0.502

Overview

Basic information about this protein and its source genome.

Accession: KP13_32247
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45073.1 gapA
Status: annotated
Amino acids: 331
Structure source: AlphaFold + ColabFold

1.2.1.-

GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. 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:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. GO:0006006 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. GO:0004365 Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+. GO:0072524 The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 69.685
Human E-value: 7.91e-128
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 96.375
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 98.37

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 0.502

Structure A0A0H3GN34

Pocket Pocket 2

P2Rank 0.78

Structure A0A0H3GN34

Pocket Pocket 1

ColabFold model

FPocket 0.36 · Pocket 30

P2Rank 0.773 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1853 / 4744 genomes with a hit

Normalized 0.391

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)

1.2.1.-

Gene Ontology (GO)

GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
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:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
GO:0006006 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
GO:0004365 Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
GO:0072524 The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
149	314	FunFam	G3DSA:3.30.360.10:FF:000001	Glyceraldehyde-3-phosphate dehydrogenase
4	324	NCBIfam	TIGR01534	glyceraldehyde-3-phosphate dehydrogenase, type I
4	324	InterPro	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I
3	326	Gene3D	G3DSA:3.40.50.720	-
148	155	ProSitePatterns	PS00071	Glyceraldehyde 3-phosphate dehydrogenase active site.
148	155	InterPro	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site
149	314	Gene3D	G3DSA:3.30.360.10	Dihydrodipicolinate Reductase; domain 2
3	166	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
3	166	InterPro	IPR036291	NAD(P)-binding domain superfamily
3	150	SMART	SM00846	gp_dh_n_7
3	150	InterPro	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
3	102	Pfam	PF00044	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
3	102	InterPro	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
2	331	PANTHER	PTHR10836	GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
2	331	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
149	312	SUPERFAMILY	SSF55347	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
144	162	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
144	162	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
171	187	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
171	187	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
109	122	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
109	122	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
268	283	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
268	283	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
228	245	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
228	245	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
3	157	FunFam	G3DSA:3.40.50.720:FF:000001	Glyceraldehyde-3-phosphate dehydrogenase
1	331	PIRSF	PIRSF000149	GAPDH
1	331	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
155	312	Pfam	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
155	312	InterPro	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain

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_A0A0H3GN34	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_32247	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
2				0.502
5				0.224

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	10.96	0.588
2	1.66	0.028
3	0.86	0.003

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
30				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	11.6	0.617
2	2.46	0.067
3	1.91	0.039

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.

61 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
9HB	6LGM	P16858	146.1 Da LogP 0.11 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)OC`
APR	1IHY	P56649	559.3 Da LogP -3.28 TPSA 291.5	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
AW9	6IQ6	P04406	130.1 Da LogP -0.20 TPSA 63.6	✓ Ro5	✓ Clean	`COC(=O)C=CC(=O)O`
F4F	6M61	P04406	282.3 Da LogP 1.60 TPSA 83.8	✓ Ro5	✓ Clean	`CC(C)[C@H]1CC[C@]([C@@H]2[C@@H]1C=C(COC2=O)C(=O…`
G3P	1DC4	P0A9B2	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C([C@H](COP(=O)(O)O)O)O`
PHN	5TSO	P00355	180.2 Da LogP 2.78 TPSA 25.8	✓ Ro5	✓ Clean	`c1cc2ccc3cccnc3c2nc1`
SND	1IHX	P56649	679.5 Da LogP -3.11 TPSA 304.0	3 viol.	✓ Clean	`c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…`
XPE	6YND	P04406	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL3559427	P04406	7.00	936.8 Da LogP 0.98 TPSA 325.2	3 viol.	✓ Clean	`COc1cccc(C(=O)NC2C(O)[C@@H](COP(=O)([O-])OP(=O)…`
CHEMBL3585922	P04406	—	280.3 Da LogP 1.62 TPSA 76.1	✓ Ro5	✓ Clean	`CC(C)[C@H]1CC[C@@]2(CO2)[C@H]2C(=O)OCC(C(=O)O)=…`
CHEMBL63507	P46406	—	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O…`

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`
ZINC15272438	1.000	280.3 Da LogP 1.62 TPSA 76.1	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CC[C@]2(CO2)[C@H]2C(=O)OCC(C(=O)O)=…`
ZINC257452854	1.000	280.3 Da LogP 1.62 TPSA 76.1	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CC[C@]2(CO2)[C@H]2C(=O)OCC(C(=O)O)=…`
ZINC257452855	1.000	280.3 Da LogP 1.62 TPSA 76.1	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CC[C@]2(CO2)[C@@H]2C(=O)OCC(C(=O)O)…`
ZINC3872731	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O…`
ZINC3872732	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC3872733	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC3872734	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
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`
ZINC5761434	1.000	280.3 Da LogP 1.62 TPSA 76.1	✓ Ro5	✓ Clean	`CC(C)[C@H]1CC[C@@]2(CO2)[C@H]2C(=O)OCC(C(=O)O)=…`
ZINC85550763	1.000	280.3 Da LogP 1.62 TPSA 76.1	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CC[C@]2(CO2)[C@@H]2C(=O)OCC(C(=O)O)…`
ZINC12360002	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC1714651	0.813	202.2 Da LogP 0.46 TPSA 69.7	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)CCC(=O)OC`
ZINC13518964	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.768	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC105372833	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC1532230	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4556979	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4556980	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4556981	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=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.