Protein profile

PA3337

ADP-L-glycero-D-mannoheptose-6-epimerase

Genome: NC_002516.2

Gene: rfaD PA3337 hldD Structure source: AlphaFold UniProt Q9HYQ8

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Amino acids 332

Annotations 6

Features 18

PDB binders 5

Druggability 0.791

Overview

Basic information about this protein and its source genome.

Accession: PA3337
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: rfaD PA3337 hldD
Status: annotated
Amino acids: 332
Structure source: AlphaFold

5.1.3.20

GO:0008712 Catalysis of the reaction: ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose. 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:0097171 The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate. GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 24.306
Human E-value: 2.35e-06
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.791

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

5.1.3.20

Gene Ontology (GO)

GO:0008712 Catalysis of the reaction: ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose.
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:0097171 The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
4	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
5	243	Pfam	PF01370	NAD dependent epimerase/dehydratase family
5	243	InterPro	IPR001509	NAD-dependent epimerase/dehydratase
15	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
22	332	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	328	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
1	328	InterPro	IPR036291	NAD(P)-binding domain superfamily
5	328	CDD	cd05248	ADP_GME_SDR_e
5	328	InterPro	IPR011912	ADP-L-glycero-D-manno-heptose-6-epimerase
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
3	330	PANTHER	PTHR43103	NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE
1	21	Phobius	SIGNAL_PEPTIDE	Signal peptide region
169	311	Gene3D	G3DSA:3.90.25.10	-
4	331	Hamap	MF_01601	ADP-L-glycero-D-manno-heptose-6-epimerase [hldD].
4	331	InterPro	IPR011912	ADP-L-glycero-D-manno-heptose-6-epimerase
6	324	Gene3D	G3DSA:3.40.50.720	-
5	330	NCBIfam	TIGR02197	ADP-glyceromanno-heptose 6-epimerase
5	330	InterPro	IPR011912	ADP-L-glycero-D-manno-heptose-6-epimerase

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
AlphaFold PA3337	AlphaFold	—	—	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
1				0.791

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.

56 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
ADQ	1EQ2	P67910	589.3 Da LogP -3.92 TPSA 311.7	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
EPZ	6DNT	D3E402	679.4 Da LogP -4.15 TPSA 332.2	3 viol.	✓ Clean	`C[C@H](C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]…`
UD1	6WJ9	Q4KCF6	607.4 Da LogP -4.65 TPSA 305.9	3 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…`
UD2	6WJA	Q4KCF6	607.4 Da LogP -4.65 TPSA 305.9	3 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](…`
UPG	4ZRN	Q9WYX9	566.3 Da LogP -4.79 TPSA 297.0	3 viol.	✓ Clean	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`

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
CHEMBL1172557	Q8T8E9	6.05	644.7 Da LogP 8.49 TPSA 132.8	2 viol.	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1C(=O)Nc1ccc2c(c1)Cc1cc(N…`

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
ZINC12959005	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC12959016	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O…`
ZINC13548378	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726233	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC3861755	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875256	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC3875257	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875258	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC88466482	0.729	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC35636069	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655887	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655889	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC44460318	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC4490939	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585026	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585028	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC8585030	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585032	0.724	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC102211562	0.698	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC110347779	0.698	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC110347782	0.698	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC97976147	0.698	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC1698877	0.689	373.4 Da LogP 3.91 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c(C(=O)Nc2ccc3c(c2)Cc2ccccc2…`
ZINC259749	0.674	303.3 Da LogP 4.65 TPSA 29.1	✓ Ro5	✓ Clean	`O=C(Nc1ccc2c(c1)Cc1ccccc1-2)c1ccccc1F`
ZINC4103659	0.674	299.4 Da LogP 4.82 TPSA 29.1	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)Nc1ccc2c(c1)Cc1ccccc1-2`
ZINC4188096	0.661	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.661	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.661	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.661	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC1233232	0.659	285.3 Da LogP 4.51 TPSA 29.1	✓ Ro5	✓ Clean	`O=C(Nc1ccc2c(c1)Cc1ccccc1-2)c1ccccc1`
ZINC12503831	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC12503833	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC13512000	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC1532538	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC2026984	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC2123545	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC2606131	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC36377965	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC3870257	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3870258	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC3870259	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3870260	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC9235501	0.655	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H…`
ZINC1210238	0.649	317.3 Da LogP 4.30 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1C(=O)Nc1ccccc1`
ZINC2047673	0.644	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC3201876	0.644	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878	0.644	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178	0.644	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC4048240	0.644	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC895113	0.644	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`

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.