Protein profile

KP13_05339

Aconitate hydratase 1

Genome: KpKP13

Gene: acnA AHE44986.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRP5

Export view

Amino acids 890

Annotations 0

Features 46

PDB binders 11

Druggability 0.824

Overview

Basic information about this protein and its source genome.

Accession: KP13_05339
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: acnA AHE44986.1
Status: annotated
Amino acids: 890
Structure source: AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 53.125
Human E-value: 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 62.946
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.0

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 0.824

Structure A0A0H3GRP5

Pocket Pocket 23

P2Rank 0.787

Structure A0A0H3GRP5

Pocket Pocket 1

ColabFold model

FPocket 0.772 · Pocket 21

P2Rank 0.827 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 451 / 4744 genomes with a hit

Normalized 0.095

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

46 records

Show feature table

Start	End	DB	Term	Name
653	890	FunFam	G3DSA:3.20.19.10:FF:000001	Aconitate hydratase
493	506	ProSitePatterns	PS01244	Aconitase family signature 2.
493	506	InterPro	IPR018136	Aconitase family, 4Fe-4S cluster binding site
630	889	SUPERFAMILY	SSF52016	LeuD/IlvD-like
10	625	SUPERFAMILY	SSF53732	Aconitase iron-sulfur domain
10	625	InterPro	IPR036008	Aconitase, iron-sulfur domain
691	818	Pfam	PF00694	Aconitase C-terminal domain
691	818	InterPro	IPR000573	Aconitase A/isopropylmalate dehydratase small subunit, swivel domain
592	650	Gene3D	G3DSA:6.10.190.10	-
14	889	PANTHER	PTHR11670	ACONITASE/IRON-RESPONSIVE ELEMENT FAMILY MEMBER
14	889	InterPro	IPR006249	Aconitase/Iron-responsive element-binding protein 2
653	890	Gene3D	G3DSA:3.20.19.10	Aconitase, domain 4
653	890	InterPro	IPR015928	Aconitase/3-isopropylmalate dehydratase, swivel
373	590	Gene3D	G3DSA:3.30.499.10	Aconitase, domain 3
373	590	InterPro	IPR015931	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3
85	564	CDD	cd01586	AcnA_IRP
6	372	Gene3D	G3DSA:3.30.499.10	Aconitase, domain 3
6	372	InterPro	IPR015931	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3
373	590	FunFam	G3DSA:3.30.499.10:FF:000009	Aconitate hydratase
5	372	FunFam	G3DSA:3.30.499.10:FF:000002	Aconitate hydratase
18	890	NCBIfam	TIGR01341	aconitate hydratase AcnA
18	890	InterPro	IPR006249	Aconitase/Iron-responsive element-binding protein 2
69	562	Pfam	PF00330	Aconitase family (aconitate hydratase)
69	562	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
217	232	PRINTS	PR00415	Aconitase family signature
217	232	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
431	442	PRINTS	PR00415	Aconitase family signature
431	442	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
203	216	PRINTS	PR00415	Aconitase family signature
203	216	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
493	506	PRINTS	PR00415	Aconitase family signature
493	506	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
279	292	PRINTS	PR00415	Aconitase family signature
279	292	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
293	306	PRINTS	PR00415	Aconitase family signature
293	306	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
170	178	PRINTS	PR00415	Aconitase family signature
170	178	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
372	386	PRINTS	PR00415	Aconitase family signature
372	386	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
146	159	PRINTS	PR00415	Aconitase family signature
146	159	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
427	443	ProSitePatterns	PS00450	Aconitase family signature 1.
427	443	InterPro	IPR018136	Aconitase family, 4Fe-4S cluster binding site
667	836	CDD	cd01580	AcnA_IRP_Swivel
667	836	InterPro	IPR044137	Aconitase A, swivel domain

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...

Legend High Medium Low

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_A0A0H3GRP5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05339	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
23				0.824
26				0.698

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	8.16	0.434
2	7.32	0.382
3	5.32	0.25
4	5.25	0.245
5	4.9	0.22

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
21				0.772
49				0.439

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	14.51	0.725
2	7.34	0.384
3	6.4	0.323
4	5.4	0.256
5	5.31	0.25

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.

25 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
ATH	1FGH	P20004	187.1 Da LogP -5.48 TPSA 140.6	✓ Ro5	✓ Clean	`C(=C(/[C@H](C(=O)[O-])O)\C(=O)[O-])/C(=O)[O-]`
F3S	5ACN	P16276	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
FLC	1B0K	P16276	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
ICT	1B0J	P16276	192.1 Da LogP -1.39 TPSA 132.1	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)O)O)C(=O)O)C(=O)O`
KP1	4KP1	P81291	132.2 Da LogP 0.92 TPSA 40.5	✓ Ro5	✓ Clean	`CC(C)(CC(C)(C)O)O`
MIC	1AMI	P20004	206.2 Da LogP -1.00 TPSA 132.1	✓ Ro5	✓ Clean	`C[C@@]([C@H](CC(=O)O)C(=O)O)(C(=O)O)O`
NIC	8ACN	P20004	193.1 Da LogP -1.45 TPSA 138.0	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)O)O)[N+](=O)[O-])C(=O)O`
NTC	1NIS	P20004	193.1 Da LogP -1.45 TPSA 138.0	✓ Ro5	✓ Clean	`C(C(=O)O)[C@@](C[N+](=O)[O-])(C(=O)O)O`
O	1B0K	P16276	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
TRA	1ACO	P20004	171.1 Da LogP -4.45 TPSA 120.4	✓ Ro5	✓ Clean	`C(/C(=C\C(=O)[O-])/C(=O)[O-])C(=O)[O-]`
TRC	5ACN	P16276	176.1 Da LogP -0.36 TPSA 111.9	✓ Ro5	✓ Clean	`C(C(CC(=O)O)C(=O)O)C(=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
ZINC1577651	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC1623550	0.529	240.1 Da LogP 2.00 TPSA 40.5	✓ Ro5	✓ Clean	`CC(C)(O)CC(O)(C(F)(F)F)C(F)(F)F`
ZINC45068939	0.519	252.2 Da LogP 1.14 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)C[C@H](CC(=O)c1ccc(O)cc1)C(=O)O`
ZINC45068942	0.519	252.2 Da LogP 1.14 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](CC(=O)c1ccc(O)cc1)C(=O)O`
ZINC168333116	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)[C@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC168342027	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)[C@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC33992595	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)[C@@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC34050089	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)[C@@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC1532902	0.500	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.500	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC4212247	0.500	292.1 Da LogP -1.16 TPSA 189.7	1 viol.	✓ Clean	`O=C(O)C[C@@H](C(=O)O)C(P(=O)(O)O)P(=O)(O)O`
ZINC5131772	0.500	292.1 Da LogP -1.16 TPSA 189.7	1 viol.	✓ Clean	`O=C(O)C[C@H](C(=O)O)C(P(=O)(O)O)P(=O)(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.