Protein profile

KP13_02159

D-erythrose-4-phosphate dehydrogenase

Genome: KpKP13

Gene: AHE42731.1 epd Structure source: AlphaFold + ColabFold UniProt A0A0H3GSZ3

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Amino acids 342

Annotations 7

Features 33

PDB binders 8

Druggability 0.7

Overview

Basic information about this protein and its source genome.

Accession: KP13_02159
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42731.1 epd
Status: annotated
Amino acids: 342
Structure source: AlphaFold + ColabFold

1.2.1.72

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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:0048001 Catalysis of the reaction: D-erythrose 4-phosphate + H2O + NAD+ = 4-phospho-D-erythronate + 2 H+ + NADH. GO:0042823 The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6. 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:0008615 The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 38.983
Human E-value: 1.8e-32
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 53.03
DEG E-value: 7.55e-127
Localization: Cytoplasmic
ColabFold pLDDT: 96.56

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 0.7

Structure A0A0H3GSZ3

Pocket Pocket 8

P2Rank 0.685

Structure A0A0H3GSZ3

Pocket Pocket 1

ColabFold model

FPocket 0.894 · Pocket 1

P2Rank 0.793 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 186 / 4744 genomes with a hit

Normalized 0.039

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)

1.2.1.72

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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:0048001 Catalysis of the reaction: D-erythrose 4-phosphate + H2O + NAD+ = 4-phospho-D-erythronate + 2 H+ + NADH.
GO:0042823 The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
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:0008615 The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
3	104	Pfam	PF00044	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
3	104	InterPro	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
3	328	Gene3D	G3DSA:3.40.50.720	-
160	316	Pfam	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
160	316	InterPro	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain
1	334	PANTHER	PTHR43148	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2
1	334	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
4	328	NCBIfam	TIGR01532	erythrose-4-phosphate dehydrogenase
4	328	InterPro	IPR006422	D-erythrose-4-phosphate dehydrogenase
1	337	PIRSF	PIRSF000149	GAPDH
1	337	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
2	337	Hamap	MF_01640	D-erythrose-4-phosphate dehydrogenase [epd].
2	337	InterPro	IPR006422	D-erythrose-4-phosphate dehydrogenase
1	179	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
1	179	InterPro	IPR036291	NAD(P)-binding domain superfamily
154	318	FunFam	G3DSA:3.30.360.10:FF:000007	D-erythrose-4-phosphate dehydrogenase
3	164	FunFam	G3DSA:3.40.50.720:FF:000001	Glyceraldehyde-3-phosphate dehydrogenase
3	155	SMART	SM00846	gp_dh_n_7
3	155	InterPro	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
155	317	SUPERFAMILY	SSF55347	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
232	249	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
232	249	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
176	192	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
176	192	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
112	125	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
112	125	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
149	167	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
149	167	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
272	287	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
272	287	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
153	160	ProSitePatterns	PS00071	Glyceraldehyde 3-phosphate dehydrogenase active site.
153	160	InterPro	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site
154	318	Gene3D	G3DSA:3.30.360.10	Dihydrodipicolinate Reductase; domain 2

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_A0A0H3GSZ3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02159	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
8				0.7

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				10.19	0.548
2				1.58	0.025

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				0.894

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	13.0	0.671
2	1.38	0.017
3	0.91	0.004

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.

60 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
3CD	2XF8	P0A9B6	697.9 Da LogP -1.69 TPSA 292.2	3 viol.	✓ Clean	`c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…`
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…`
G3H	1NQO	P00362	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C([C@H](C=O)O)OP(=O)(O)O`
G3P	1DC4	P0A9B2	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C([C@H](COP(=O)(O)O)O)O`
MLI	6GFP	Q8DIW5	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
PHN	5TSO	P00355	180.2 Da LogP 2.78 TPSA 25.8	✓ Ro5	✓ Clean	`c1cc2ccc3cccnc3c2nc1`
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)=…`

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)…`
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)…`
ZINC238950253	0.756	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950256	0.756	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950259	0.756	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950261	0.756	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC231965	0.696	214.7 Da LogP 3.44 TPSA 25.8	✓ Ro5	✓ Clean	`Clc1ccc2ccc3cccnc3c2n1`
ZINC40442691	0.696	259.1 Da LogP 3.55 TPSA 25.8	✓ Ro5	✓ Clean	`Brc1ccc2ccc3cccnc3c2n1`
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`
ZINC12360002	0.644	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	0.644	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	0.644	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	0.644	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	0.644	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.644	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	0.644	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586022	0.644	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`

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.