Protein profile

KP13_31947

2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase

Genome: KpKP13

Gene: AHE45025.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN96

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Amino acids 253

Annotations 5

Features 27

PDB binders 6

Druggability 0.491

Overview

Basic information about this protein and its source genome.

Accession: KP13_31947
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45025.1
Status: annotated
Amino acids: 253
Structure source: AlphaFold + ColabFold

1.1.1.127

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:0008678 Catalysis of the reaction: 2-deoxy-D-gluconate + NAD+ = 3-dehydro-2-deoxy-D-gluconate + NADH + H+. 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:0047001 Catalysis of the reaction: NAD+ + 2-dehydro-3-deoxy-D-gluconate = NADH + (4S)-4,6-dihydroxy-2,5-dioxohexanoate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.662
Human E-value: 8.25e-09
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 42.802
DEG E-value: 6.480000000000001e-64
Localization: Cytoplasmic
ColabFold pLDDT: 97.42

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 0.491

Structure A0A0H3GN96

Pocket Pocket 8

P2Rank 0.887

Structure A0A0H3GN96

Pocket Pocket 1

ColabFold model

FPocket 0.725 · Pocket 2

P2Rank 0.924 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 273 / 4744 genomes with a hit

Normalized 0.058

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1.1.1.127

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:0008678 Catalysis of the reaction: 2-deoxy-D-gluconate + NAD+ = 3-dehydro-2-deoxy-D-gluconate + NADH + H+.
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:0047001 Catalysis of the reaction: NAD+ + 2-dehydro-3-deoxy-D-gluconate = NADH + (4S)-4,6-dihydroxy-2,5-dioxohexanoate.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records

Show feature table

Start	End	DB	Term	Name
158	177	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
158	177	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
84	95	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
84	95	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
138	146	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
138	146	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
6	252	CDD	cd05347	Ga5DH-like_SDR_c
145	173	ProSitePatterns	PS00061	Short-chain dehydrogenases/reductases family signature.
145	173	InterPro	IPR020904	Short-chain dehydrogenase/reductase, conserved site
6	252	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
6	252	InterPro	IPR036291	NAD(P)-binding domain superfamily
4	250	PANTHER	PTHR42760	SHORT-CHAIN DEHYDROGENASES/REDUCTASES FAMILY MEMBER
1	253	FunFam	G3DSA:3.40.50.720:FF:000081	2-deoxy-D-gluconate 3-dehydrogenase
20	250	Pfam	PF13561	Enoyl-(Acyl carrier protein) reductase
6	253	NCBIfam	TIGR01832	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
6	253	InterPro	IPR011286	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase
1	253	Gene3D	G3DSA:3.40.50.720	-
158	177	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
132	148	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
132	148	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
179	196	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
179	196	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
12	29	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
12	29	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
84	95	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
214	234	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
214	234	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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_A0A0H3GN96	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31947	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				0.192
15				0.083
5				0.004
16				0.0

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				28.06	0.887
2				1.71	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
2				0.725
1				0.538

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				15.56	0.756
2				5.25	0.245

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
3HL	2ZTL	Q5KST5	104.1 Da LogP -0.16 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)O)O`
3HR	3VDR	D0VWQ0	104.1 Da LogP -0.16 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](CC(=O)O)O`
AAE	3VDR	D0VWQ0	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CC(=O)O`
DXX	3W8D	D0VWQ0	118.1 Da LogP -0.21 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C(=O)O)C(=O)O`
MLA	3W8F	D0VWQ0	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
TLA	5U9P	B4EEX4	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
KDH	Q8I2S7	6.50	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`c1c(cc(c(c1O)O)O)[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)…`
LU2	Q965D6	6.10	286.2 Da LogP 2.28 TPSA 111.1	✓ Ro5	Alert	`c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O`
CHEMBL129451	Q965D6	6.00	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c…`
CHEMBL36327	Q965D6	6.00	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)…`
NAR	Q965D6	—	272.3 Da LogP 2.51 TPSA 87.0	✓ Ro5	✓ Clean	`c1cc(ccc1[C@@H]2CC(=O)c3c(cc(cc3O2)O)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
ZINC156701	1.000	272.3 Da LogP 2.51 TPSA 87.0	✓ Ro5	✓ Clean	`O=C1C[C@@H](c2ccc(O)cc2)Oc2cc(O)cc(O)c21`
ZINC1785	1.000	272.3 Da LogP 2.51 TPSA 87.0	✓ Ro5	✓ Clean	`O=C1C[C@H](c2ccc(O)cc2)Oc2cc(O)cc(O)c21`
ZINC18185774	1.000	286.2 Da LogP 2.28 TPSA 111.1	✓ Ro5	Alert	`O=c1cc(-c2ccc(O)c(O)c2)oc2cc(O)cc(O)c12`
ZINC3870412	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…`
ZINC3870413	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…`
ZINC3870414	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…`
ZINC3870415	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…`
ZINC14436185	0.854	472.4 Da LogP 2.54 TPSA 186.4	2 viol.	Alert	`COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…`
ZINC3978503	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)…`
ZINC4534390	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)c…`
ZINC4544252	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c1…`
ZINC8681494	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c…`
ZINC14727965	0.848	426.4 Da LogP 2.82 TPSA 156.9	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)cc1)…`
ZINC4935	0.816	256.3 Da LogP 2.80 TPSA 66.8	✓ Ro5	✓ Clean	`O=C1C[C@H](c2ccccc2)Oc2cc(O)cc(O)c21`
ZINC73693	0.816	256.3 Da LogP 2.80 TPSA 66.8	✓ Ro5	✓ Clean	`O=C1C[C@@H](c2ccccc2)Oc2cc(O)cc(O)c21`
ZINC14728393	0.806	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	✓ Clean	`O=C1C[C@@H](c2cc(O)cc(O)c2)Oc2cc(O)cc(O)c21`
ZINC58116	0.795	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	Alert	`O=C1C[C@H](c2ccc(O)c(O)c2)Oc2cc(O)cc(O)c21`
ZINC58117	0.795	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	Alert	`O=C1C[C@@H](c2ccc(O)c(O)c2)Oc2cc(O)cc(O)c21`
ZINC3871576	0.778	270.2 Da LogP 2.58 TPSA 90.9	✓ Ro5	✓ Clean	`O=c1cc(-c2ccc(O)cc2)oc2cc(O)cc(O)c12`
ZINC4348965	0.775	270.3 Da LogP 3.11 TPSA 66.8	✓ Ro5	✓ Clean	`Cc1cc(O)c2c(c1)O[C@H](c1ccc(O)cc1)CC2=O`
ZINC4348970	0.775	270.3 Da LogP 3.11 TPSA 66.8	✓ Ro5	✓ Clean	`Cc1cc(O)c2c(c1)O[C@@H](c1ccc(O)cc1)CC2=O`
ZINC2146973	0.762	286.3 Da LogP 2.81 TPSA 76.0	✓ Ro5	✓ Clean	`COc1ccc([C@@H]2CC(=O)c3c(O)cc(O)cc3O2)cc1`
ZINC895707	0.762	286.3 Da LogP 2.81 TPSA 76.0	✓ Ro5	✓ Clean	`COc1ccc([C@H]2CC(=O)c3c(O)cc(O)cc3O2)cc1`
ZINC21992193	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…`
ZINC21992196	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…`
ZINC21992198	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…`
ZINC21992201	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…`
ZINC14813714	0.750	300.3 Da LogP 2.59 TPSA 100.1	✓ Ro5	Alert	`COc1cc(O)c2c(=O)cc(-c3ccc(O)c(O)c3)oc2c1`
ZINC338283	0.738	286.3 Da LogP 2.81 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(O)c2c(c1)O[C@@H](c1ccc(O)cc1)CC2=O`
ZINC338284	0.738	286.3 Da LogP 2.81 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(O)c2c(c1)O[C@H](c1ccc(O)cc1)CC2=O`
ZINC13520048	0.730	302.2 Da LogP 1.99 TPSA 131.4	✓ Ro5	Alert	`O=c1cc(-c2cc(O)c(O)c(O)c2)oc2cc(O)cc(O)c12`
ZINC39317	0.730	270.2 Da LogP 2.58 TPSA 90.9	✓ Ro5	Alert	`O=c1cc(-c2ccc(O)c(O)c2)oc2cccc(O)c12`
ZINC14728050	0.725	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	✓ Clean	`O=C1C[C@@H](c2ccc(O)cc2O)Oc2cc(O)cc(O)c21`
ZINC14728051	0.725	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	✓ Clean	`O=C1C[C@H](c2ccc(O)cc2O)Oc2cc(O)cc(O)c21`
ZINC14642643	0.722	456.4 Da LogP 2.83 TPSA 166.1	1 viol.	Alert	`COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…`
ZINC6536308	0.718	288.7 Da LogP 3.52 TPSA 70.7	✓ Ro5	✓ Clean	`O=c1cc(-c2ccc(Cl)cc2)oc2cc(O)cc(O)c12`
ZINC14813748	0.714	300.3 Da LogP 2.59 TPSA 100.1	✓ Ro5	Alert	`COc1cc(O)cc2oc(-c3ccc(O)c(O)c3)cc(=O)c12`
ZINC519621	0.714	300.3 Da LogP 2.59 TPSA 100.1	✓ Ro5	✓ Clean	`COc1cc(-c2cc(=O)c3c(O)cc(O)cc3o2)ccc1O`
ZINC5733652	0.714	300.3 Da LogP 2.59 TPSA 100.1	✓ Ro5	✓ Clean	`COc1ccc(-c2cc(=O)c3c(O)cc(O)cc3o2)cc1O`
ZINC3872070	0.711	254.2 Da LogP 2.87 TPSA 70.7	✓ Ro5	✓ Clean	`O=c1cc(-c2ccccc2)oc2cc(O)cc(O)c12`
ZINC14728095	0.700	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	✓ Clean	`O=C1C[C@H](c2c(O)cccc2O)Oc2cc(O)cc(O)c21`
ZINC6091723	0.700	288.3 Da LogP 2.22 TPSA 107.2	✓ Ro5	✓ Clean	`O=C1C[C@@H](c2c(O)cccc2O)Oc2cc(O)cc(O)c21`
ZINC14757037	0.698	366.3 Da LogP 1.76 TPSA 154.5	✓ Ro5	Alert	`O=c1cc(-c2ccc(O)c(O)c2)oc2cc(OS(=O)(=O)O)cc(O)c…`
ZINC5999024	0.698	286.3 Da LogP 2.81 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(O)cc2c1C(=O)C[C@H](c1ccc(O)cc1)O2`
ZINC5999025	0.698	286.3 Da LogP 2.81 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(O)cc2c1C(=O)C[C@@H](c1ccc(O)cc1)O2`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=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.