Protein profile

VK055_4383

glucarate dehydratase

Genome: KpATCC43816

Gene: AIK82926.1 gudD Structure source: AlphaFold + ColabFold UniProt A0A0H3GXH9

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Amino acids 435

Annotations 3

Features 24

PDB binders 7

Druggability 0.944

Overview

Basic information about this protein and its source genome.

Accession: VK055_4383
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82926.1 gudD
Status: annotated
Amino acids: 435
Structure source: AlphaFold + ColabFold

GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 22.762
Localization: Cytoplasmic
ColabFold pLDDT: 98.25

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 0.944

Structure A0A0H3GXH9

Pocket Pocket 1

P2Rank 0.941

Structure A0A0H3GXH9

Pocket Pocket 1

ColabFold model

FPocket 0.867 · Pocket 22

P2Rank 0.936 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 182 / 4744 genomes with a hit

Normalized 0.038

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
100	125	ProSitePatterns	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.
100	125	InterPro	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site
126	386	FunFam	G3DSA:3.20.20.120:FF:000003	Glucarate dehydratase
19	401	PANTHER	PTHR48080	D-GALACTONATE DEHYDRATASE-RELATED
19	401	InterPro	IPR034593	D-galactonate dehydratase DgoD-like
127	403	SUPERFAMILY	SSF51604	Enolase C-terminal domain-like
127	403	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
1	402	Gene3D	G3DSA:3.30.390.10	-
1	402	InterPro	IPR029017	Enolase-like, N-terminal
173	273	SMART	SM00922	MR_MLE_2
173	273	InterPro	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal
1	434	SFLD	SFLDF00005	glucarate dehydratase
1	434	InterPro	IPR034598	D-Glucarate dehydratase-like
28	125	Pfam	PF02746	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
28	125	InterPro	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain
1	405	CDD	cd03323	D-glucarate_dehydratase
1	405	InterPro	IPR034598	D-Glucarate dehydratase-like
126	386	Gene3D	G3DSA:3.20.20.120	-
126	386	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
1	434	SFLD	SFLDS00001	Enolase
1	125	SUPERFAMILY	SSF54826	Enolase N-terminal domain-like
1	125	InterPro	IPR029017	Enolase-like, N-terminal
177	394	Pfam	PF13378	Enolase C-terminal domain-like
177	394	InterPro	IPR029065	Enolase C-terminal domain-like

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_A0A0H3GXH9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4383	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				0.944
5				0.918
2				0.688

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	28.26	0.924
2	7.76	0.411
3	2.16	0.051
4	1.68	0.029

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
22				0.867
3				0.287

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	26.98	0.918
2	6.94	0.358
3	2.08	0.047
4	1.82	0.034

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.

57 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
DTT	4G8T	A6VQF1	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
DTU	4G8T	A6VQF1	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@H]([C@H](CS)O)O)S`
DXG	1ECQ	P0AES2	192.1 Da LogP -5.04 TPSA 140.9	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)[O-])O)O)[C@@H](C(=O)[O-])O`
GKR	3PFR	A6VQF6	208.1 Da LogP -6.07 TPSA 161.2	✓ Ro5	✓ Clean	`[C@H]([C@@H]([C@@H](C(=O)[O-])O)O)([C@H](C(=O)[…`
GLR	1EC8	P0AES2	190.1 Da LogP -4.83 TPSA 137.8	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)[O-])O)O)C(=O)C(=O)[O-]`
TLA	4IT1	Q3KB33	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`
XYH	1EC9	P0AES2	194.1 Da LogP -4.68 TPSA 150.1	✓ Ro5	✓ Clean	`[C@H]([C@@H](C(=O)NO)O)([C@H](C(=O)[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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
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`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
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`
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`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
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`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`

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.