Protein profile

PA5164

dTDP-4-dehydrorhamnose 3,5-epimerase

Genome: NC_002516.2

Gene: PA5164 rmlC Structure source: Experimental + AlphaFold UniProt Q9HU21

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Amino acids 181

Annotations 7

Features 13

PDB binders 8

Druggability 0.346

Overview

Basic information about this protein and its source genome.

Accession: PA5164
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5164 rmlC
Status: annotated
Amino acids: 181
Structure source: Experimental + AlphaFold

5.1.3.13

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008830 Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose. GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate. GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues. GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Unknown

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 0.346

Structure –

Pocket –

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)

5.1.3.13

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008830 Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
3	170	CDD	cd00438	cupin_RmlC
3	170	InterPro	IPR000888	dTDP-4-dehydrorhamnose 3,5-epimerase-related
3	177	NCBIfam	TIGR01221	dTDP-4-dehydrorhamnose 3,5-epimerase
3	177	InterPro	IPR000888	dTDP-4-dehydrorhamnose 3,5-epimerase-related
1	181	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
1	181	InterPro	IPR014710	RmlC-like jelly roll fold
6	175	Pfam	PF00908	dTDP-4-dehydrorhamnose 3,5-epimerase
6	175	InterPro	IPR000888	dTDP-4-dehydrorhamnose 3,5-epimerase-related
1	178	SUPERFAMILY	SSF51182	RmlC-like cupins
1	178	InterPro	IPR011051	RmlC-like cupin domain superfamily
2	176	PANTHER	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE
2	176	InterPro	IPR000888	dTDP-4-dehydrorhamnose 3,5-epimerase-related
1	181	FunFam	G3DSA:2.60.120.10:FF:000051	dTDP-4-dehydrorhamnose 3,5-epimerase

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

5 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 2IXK	X-ray	1.70 Å	A,B	100.0% 1-181	PDBe RCSB PDBj File	Viewing
PDB 2IXI	X-ray	1.80 Å	A,B	100.0% 1-181	PDBe RCSB PDBj File	Loaded
PDB 2IXH	X-ray	2.00 Å	A,B	100.0% 1-181	PDBe RCSB PDBj File	Loaded
PDB 1RTV	X-ray	2.50 Å	A	100.0% 1-181	PDBe RCSB PDBj File	Loaded
PDB 2IXJ	X-ray	2.54 Å	A	100.0% 1-181	PDBe RCSB PDBj File	Loaded
AlphaFold PA5164	AlphaFold	—	—	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
2				0.346
3				0.224

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	19.24	0.836
2	2.46	0.067
3	1.14	0.009

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				0.426
1				0.253

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.

63 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
SRT	1RTV 2.50 Å Open crystal	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@H](C(=O)O)O)(C(=O)O)O`

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
18T	4HMZ	Q5SFD1	548.3 Da LogP -2.43 TPSA 256.5	3 viol.	✓ Clean	`C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP…`
ATY	1DZT	P26394	444.2 Da LogP -0.71 TPSA 203.7	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…`
TDO	6NDR	Q5ZXH5	546.3 Da LogP -2.22 TPSA 253.4	3 viol.	✓ Clean	`C[C@H]1C(=O)[C@H]([C@H]([C@H](O1)O[P@@](=O)(O)O…`
TDR	4HN1	Q5SFD1	126.1 Da LogP -0.63 TPSA 65.7	✓ Ro5	✓ Clean	`CC1=CNC(=O)NC1=O`
THM	4HN1	Q5SFD1	242.2 Da LogP -1.51 TPSA 104.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O`
TPE	1DZT	P26394	520.3 Da LogP 1.38 TPSA 192.7	2 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…`
TYD	1EPZ	O27818	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`

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
CHEMBL592712	P9WH10	7.21	416.5 Da LogP 3.99 TPSA 81.4	✓ Ro5	✓ Clean	`C=CCn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc…`
CHEMBL589101	P9WH10	7.00	404.5 Da LogP 3.82 TPSA 81.4	✓ Ro5	✓ Clean	`CCn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc21`
CHEMBL590576	P9WH10	6.40	448.5 Da LogP 2.67 TPSA 115.5	✓ Ro5	✓ Clean	`C=CCn1c2ccccc2c2nnc(S(=O)(=O)CCCn3c(=O)[nH]c4cc…`
CHEMBL592545	P9WH10	6.30	390.5 Da LogP 3.34 TPSA 81.4	✓ Ro5	✓ Clean	`Cn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc21`
CHEMBL600648	P9WH10	6.10	436.5 Da LogP 2.51 TPSA 115.5	✓ Ro5	✓ Clean	`CCn1c2ccccc2c2nnc(S(=O)(=O)CCCn3c(=O)[nH]c4cccc…`

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
ZINC12503053	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC18094029	1.000	404.5 Da LogP 3.82 TPSA 81.4	✓ Ro5	✓ Clean	`CCn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc21`
ZINC18322375	1.000	416.5 Da LogP 3.99 TPSA 81.4	✓ Ro5	✓ Clean	`C=CCn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc…`
ZINC1842580	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2159	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2545102	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC25672	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC2572653	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC33979243	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC33979244	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC3831529	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC5765078	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC6072455	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC8215882	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC13507072	0.959	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC33979251	0.959	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC2751170	0.875	418.5 Da LogP 4.21 TPSA 81.4	✓ Ro5	✓ Clean	`CCCn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc21`
ZINC4804742	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O)…`
ZINC4804743	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O)[…`
ZINC4804744	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O…`
ZINC4804745	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O)…`
ZINC13523519	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.837	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC2745826	0.821	390.5 Da LogP 3.34 TPSA 81.4	✓ Ro5	✓ Clean	`Cn1c2ccccc2c2nnc(SCCCn3c(=O)[nH]c4ccccc43)nc21`
ZINC2995449	0.810	466.6 Da LogP 4.85 TPSA 81.4	✓ Ro5	✓ Clean	`O=c1[nH]c2ccccc2n1CCCSc1nnc2c3ccccc3n(Cc3ccccc3…`
ZINC16928956	0.810	258.3 Da LogP -0.14 TPSA 87.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=S`
ZINC5085194	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC5085195	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC5085196	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC5085197	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC111459735	0.800	481.2 Da LogP -1.20 TPSA 249.9	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC138164075	0.800	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC11677083	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](F)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC1630862	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC2130970	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC25054	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC4537463	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC4537467	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC56790	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC5833725	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC5833727	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC5833731	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC6667024	0.791	256.3 Da LogP -0.86 TPSA 93.5	✓ Ro5	✓ Clean	`COC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[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.