Protein profile

VK055_0893

3-hydroxyisobutyrate dehydrogenase

Genome: KpATCC43816

Gene: AIK79516.1 ygbJ Structure source: ColabFold

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Amino acids 205

Annotations 3

Features 12

PDB binders 8

Druggability 0.513

Overview

Basic information about this protein and its source genome.

Accession: VK055_0893
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79516.1 ygbJ
Status: annotated
Amino acids: 205
Structure source: ColabFold

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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.328
Human E-value: 1.33e-11
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 73.632
DEG E-value: 2.28e-100
Localization: Cytoplasmic
ColabFold pLDDT: 97.59

Selected Druggability evidence

ColabFold / curated 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 0.513

Structure CB_VK055_0893

Pocket Pocket 4

P2Rank 0.773

Structure CB_VK055_0893

Pocket Pocket 1

ColabFold model

FPocket 0.513 · Pocket 4

P2Rank 0.773 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 46 / 4744 genomes with a hit

Normalized 0.01

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
4	72	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
4	72	InterPro	IPR036291	NAD(P)-binding domain superfamily
73	197	SUPERFAMILY	SSF48179	6-phosphogluconate dehydrogenase C-terminal domain-like
73	197	InterPro	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
3	198	PANTHER	PTHR43060	3-HYDROXYISOBUTYRATE DEHYDROGENASE-LIKE 1, MITOCHONDRIAL-RELATED
75	194	Pfam	PF14833	NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
75	194	InterPro	IPR029154	3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain
1	72	Gene3D	G3DSA:3.40.50.720	-
75	198	Gene3D	G3DSA:1.10.1040.10	-
75	198	InterPro	IPR013328	6-phosphogluconate dehydrogenase, domain 2
3	69	Pfam	PF03446	NAD binding domain of 6-phosphogluconate dehydrogenase
3	69	InterPro	IPR006115	6-phosphogluconate dehydrogenase, NADP-binding

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 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold VK055_0893	ColabFold	—	—	full sequence	—	Viewing

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
4				0.513
6				0.372
12				0.102
1				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	Score	Probability
1	19.33	0.773
2	1.49	0.017
3	1.34	0.013

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.

58 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
3OH	5Y8O	P9WNY5	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C(CO)C(=O)O`
9ON	5Y8L	P9WNY5	146.1 Da LogP 0.57 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)O)C(=O)O`
AKR	5Y8M	P9WNY5	72.1 Da LogP 0.26 TPSA 37.3	✓ Ro5	✓ Clean	`C=CC(=O)O`
BO3	6SM7	P0A9V8	61.8 Da LogP -2.05 TPSA 60.7	✓ Ro5	✓ Clean	`B(O)(O)O`
HIU	5Y8M	P9WNY5	104.1 Da LogP -0.30 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](CO)C(=O)O`
HUI	5Y8L	P9WNY5	104.1 Da LogP -0.30 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@@H](CO)C(=O)O`
LLQ	6SMY	P0A9V8	156.2 Da LogP -1.77 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](CS(=O)(=O)O)O)O`
TLA	5XVH	A3MU08	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).

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
ZINC12359024	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`
ZINC13533920	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`
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`
ZINC3860635	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`
ZINC6072527	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`
ZINC2029340	0.591	216.3 Da LogP 2.38 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC2029341	0.591	216.3 Da LogP 2.38 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@H](CCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC2029343	0.591	216.3 Da LogP 2.38 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCC[C@H](C)C(=O)O)C(=O)O`
ZINC2029346	0.591	230.3 Da LogP 2.77 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC2029348	0.591	230.3 Da LogP 2.77 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@H](CCCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC2029350	0.591	230.3 Da LogP 2.77 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCCC[C@H](C)C(=O)O)C(=O)O`
ZINC2029355	0.591	258.4 Da LogP 3.55 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC2029358	0.591	258.4 Da LogP 3.55 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@H](CCCCCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC2029360	0.591	258.4 Da LogP 3.55 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCCCCC[C@H](C)C(=O)O)C(=O)O`
ZINC4100991	0.591	286.4 Da LogP 4.33 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCCCCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC4100995	0.591	286.4 Da LogP 4.33 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@H](CCCCCCCCCC[C@@H](C)C(=O)O)C(=O)O`
ZINC4101001	0.591	286.4 Da LogP 4.33 TPSA 74.6	✓ Ro5	✓ Clean	`C[C@@H](CCCCCCCCCC[C@H](C)C(=O)O)C(=O)O`
ZINC1560405156	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC142127993	0.571	219.2 Da LogP -1.20 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC214811896	0.571	219.2 Da LogP -1.20 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](O)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC214811946	0.571	219.2 Da LogP -1.20 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC214811999	0.571	219.2 Da LogP -1.20 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](O)C(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC13529664	0.560	320.3 Da LogP -1.08 TPSA 190.3	1 viol.	✓ Clean	`O=C(O)CC[C@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=…`
ZINC14510370	0.556	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCO`
ZINC1531061	0.556	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1610426	0.556	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCO`
ZINC2168567	0.556	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCO`
ZINC3861297	0.556	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCO`
ZINC4284502	0.556	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCO`
ZINC5287109	0.556	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCCO`
ZINC2242980	0.552	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC2560662	0.552	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC5360219	0.552	231.2 Da LogP 0.47 TPSA 103.7	✓ Ro5	✓ Clean	`CC(C)CC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC3845741	0.542	202.2 Da LogP 1.84 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C)[C@@H](CC[C@@H](C)C(=O)O)C(=O)O`
ZINC3845742	0.542	202.2 Da LogP 1.84 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C)[C@H](CC[C@@H](C)C(=O)O)C(=O)O`
ZINC3845743	0.542	202.2 Da LogP 1.84 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C)[C@@H](CC[C@H](C)C(=O)O)C(=O)O`
ZINC3845744	0.542	202.2 Da LogP 1.84 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C)[C@H](CC[C@H](C)C(=O)O)C(=O)O`
ZINC217513646	0.538	362.3 Da LogP -1.76 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@H](NC(=O)CC(=O)N[C@@H](CCC(=O)O)C(=O…`
ZINC225956904	0.538	362.3 Da LogP -1.76 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@H](NC(=O)CC(=O)N[C@H](CCC(=O)O)C(=O)…`
ZINC225956918	0.538	362.3 Da LogP -1.76 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@@H](NC(=O)CC(=O)N[C@H](CCC(=O)O)C(=O…`
ZINC58123315	0.538	376.3 Da LogP -1.36 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@H](NC(=O)CCC(=O)N[C@@H](CCC(=O)O)C(=…`
ZINC58123320	0.538	376.3 Da LogP -1.36 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@H](NC(=O)CCC(=O)N[C@H](CCC(=O)O)C(=O…`
ZINC58123326	0.538	376.3 Da LogP -1.36 TPSA 207.4	1 viol.	✓ Clean	`O=C(O)CC[C@@H](NC(=O)CCC(=O)N[C@H](CCC(=O)O)C(=…`
ZINC87491353	0.536	259.3 Da LogP -3.16 TPSA 138.5	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CN(CO)C(CO)CO`
ZINC87491354	0.536	259.3 Da LogP -3.16 TPSA 138.5	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@H](O)CN(CO)C(CO)CO`

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.