Protein profile

PA4457

arabinose-5-phosphate isomerase KdsD

Genome: NC_002516.2

Gene: kdsD PA4457 Structure source: AlphaFold UniProt Q9HVW0

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Amino acids 326

Annotations 8

Features 31

PDB binders 2

Druggability 0.497

Overview

Basic information about this protein and its source genome.

Accession: PA4457
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: kdsD PA4457
Status: annotated
Amino acids: 326
Structure source: AlphaFold

5.3.1.13

GO:0019146 Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H+. GO:0097367 Binding to a carbohydrate derivative. GO:0046872 Binding to a metal ion. 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:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. GO:1901135 The chemical reactions and pathways involving carbohydrate derivative.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.497

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

5.3.1.13

Gene Ontology (GO)

GO:0019146 Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H+.
GO:0097367 Binding to a carbohydrate derivative.
GO:0046872 Binding to a metal ion.
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:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
GO:1901135 The chemical reactions and pathways involving carbohydrate derivative.
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.

31 records

Show feature table

Start	End	DB	Term	Name
1	326	PIRSF	PIRSF004692	KdsD_KpsF
1	326	InterPro	IPR004800	Phosphosugar isomerase, KdsD/KpsF-type
274	326	ProSiteProfiles	PS51371	CBS domain profile.
274	326	InterPro	IPR000644	CBS domain
43	174	Pfam	PF01380	SIS domain
43	174	InterPro	IPR001347	SIS domain
47	316	NCBIfam	TIGR00393	KpsF/GutQ family sugar-phosphate isomerase
47	316	InterPro	IPR004800	Phosphosugar isomerase, KdsD/KpsF-type
207	265	ProSiteProfiles	PS51371	CBS domain profile.
207	265	InterPro	IPR000644	CBS domain
47	174	CDD	cd05014	SIS_Kpsf
47	174	InterPro	IPR035474	KpsF-like, SIS domain
279	323	Pfam	PF00571	CBS domain
279	323	InterPro	IPR000644	CBS domain
219	260	Pfam	PF00571	CBS domain
219	260	InterPro	IPR000644	CBS domain
11	324	SUPERFAMILY	SSF53697	SIS domain
11	324	InterPro	IPR046348	SIS domain superfamily
199	322	CDD	cd04604	CBS_pair_SIS_assoc
199	323	Gene3D	G3DSA:3.10.580.10	-
199	323	InterPro	IPR046342	CBS domain superfamily
212	260	SMART	SM00116	cbs_1
212	260	InterPro	IPR000644	CBS domain
277	325	SMART	SM00116	cbs_1
277	325	InterPro	IPR000644	CBS domain
7	197	FunFam	G3DSA:3.40.50.10490:FF:000011	Arabinose 5-phosphate isomerase
38	181	ProSiteProfiles	PS51464	SIS domain profile.
38	181	InterPro	IPR001347	SIS domain
199	323	FunFam	G3DSA:3.10.580.10:FF:000007	Arabinose 5-phosphate isomerase
1	326	PANTHER	PTHR42745	-
5	198	Gene3D	G3DSA:3.40.50.10490	-

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 + 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 PA4457	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				0.497

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.

52 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
A5P	5UQI	A0A0H2VCL5	232.1 Da LogP -2.83 TPSA 147.7	1 viol.	✓ Clean	`C([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O`
CMK	3K2V	A6TEL6	543.4 Da LogP -4.78 TPSA 293.8	3 viol.	✓ Clean	`C1[C@H]([C@H]([C@H](O[C@@]1(C(=O)O)O[P@@](=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
ZINC2516111	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3869812	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC5975509	0.760	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC25721582	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC25721586	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC4544030	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4544032	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4544034	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887586	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC8216074	0.622	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@](=O)(O)…`
ZINC8551188	0.622	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)O…`
ZINC100065511	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104864216	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@](=O)(O)OP(=O)(O)O)[C…`
ZINC12504412	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC12504413	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12504414	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431045	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431047	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC13548733	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC1530556	0.600	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC22116391	0.600	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC33913782	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC3606137	0.600	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869426	0.600	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC8215624	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC8551307	0.600	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC8551308	0.600	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC5132038	0.594	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502055	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC12502057	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12502058	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431057	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431059	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726736	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC3861746	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@@](=O)(O)…`
ZINC53683723	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC82142138	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC82142140	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12501562	0.581	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC1532623	0.581	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC3869604	0.581	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC4545928	0.581	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=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.