Protein profile

KP13_00811

GTP-binding protein lepA

Genome: KpKP13

Gene: AHE43175.1 lepA Structure source: AlphaFold + ColabFold UniProt A0A0H3H1L4

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Amino acids 599

Annotations 8

Features 53

PDB binders 8

Druggability 0.546

Overview

Basic information about this protein and its source genome.

Accession: KP13_00811
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43175.1 lepA
Status: annotated
Amino acids: 599
Structure source: AlphaFold + ColabFold

3.6.5.n1

GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate. GO:0005525 Binding to GTP, guanosine triphosphate. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0097216 Binding to guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions. GO:0043022 Binding to a ribosome. GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.943
Human E-value: 1.37e-09
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 95.492
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 88.6

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 0.546

Structure A0A0H3H1L4

Pocket Pocket 36

P2Rank 0.546

Structure A0A0H3H1L4

Pocket Pocket 1

ColabFold model

FPocket 0.901 · Pocket 1

P2Rank 0.543 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 4111 / 4744 genomes with a hit

Normalized 0.867

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)

3.6.5.n1

Gene Ontology (GO)

GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
GO:0005525 Binding to GTP, guanosine triphosphate.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0097216 Binding to guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions.
GO:0043022 Binding to a ribosome.
GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.
GO:0045727 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

53 records

Show feature table

Start	End	DB	Term	Name
5	183	CDD	cd01890	LepA
42	57	ProSitePatterns	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.
42	57	InterPro	IPR031157	Tr-type G domain, conserved site
368	478	FunFam	G3DSA:3.30.70.240:FF:000005	Elongation factor 4
191	275	CDD	cd03699	EF4_II
286	367	FunFam	G3DSA:3.30.70.870:FF:000004	Translation factor GUF1, mitochondrial
401	479	CDD	cd03709	lepA_C
401	479	InterPro	IPR035654	Elongation factor 4, domain IV
186	285	Gene3D	G3DSA:2.40.30.10	Translation factors
479	553	Gene3D	G3DSA:3.30.70.2570	-
479	553	InterPro	IPR038363	LepA, C-terminal domain superfamily
90	101	PRINTS	PR00315	GTP-binding elongation factor signature
90	101	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
126	135	PRINTS	PR00315	GTP-binding elongation factor signature
126	135	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
6	19	PRINTS	PR00315	GTP-binding elongation factor signature
6	19	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
74	84	PRINTS	PR00315	GTP-binding elongation factor signature
74	84	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
49	57	PRINTS	PR00315	GTP-binding elongation factor signature
49	57	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
1	597	Hamap	MF_00071	Elongation factor 4 [lepA].
1	597	InterPro	IPR006297	Elongation factor 4
293	368	CDD	cd16260	EF4_III
1	185	FunFam	G3DSA:3.40.50.300:FF:000078	Elongation factor 4
5	172	NCBIfam	TIGR00231	small GTP-binding protein domain
5	172	InterPro	IPR005225	Small GTP-binding protein domain
2	181	Pfam	PF00009	Elongation factor Tu GTP binding domain
2	181	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
2	184	ProSiteProfiles	PS51722	Translational (tr)-type guanine nucleotide-binding (G) domain profile.
2	184	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
399	481	Pfam	PF00679	Elongation factor G C-terminus
399	481	InterPro	IPR000640	Elongation factor EFG, domain V-like
186	285	FunFam	G3DSA:2.40.30.10:FF:000015	Translation factor GUF1, mitochondrial
2	594	NCBIfam	TIGR01393	translation elongation factor 4
2	594	InterPro	IPR006297	Elongation factor 4
1	185	Gene3D	G3DSA:3.40.50.300	-
1	185	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
479	553	FunFam	G3DSA:3.30.70.2570:FF:000001	Translation factor GUF1, mitochondrial
286	367	Gene3D	G3DSA:3.30.70.870	Elongation Factor G (Translational Gtpase), domain 3
205	275	Pfam	PF03144	Elongation factor Tu domain 2
205	275	InterPro	IPR004161	Translation elongation factor EFTu-like, domain 2
292	370	SUPERFAMILY	SSF54980	EF-G C-terminal domain-like
292	370	InterPro	IPR035647	EF-G domain III/V-like
487	592	Pfam	PF06421	GTP-binding protein LepA C-terminus
487	592	InterPro	IPR013842	GTP-binding protein LepA, C-terminal
368	478	Gene3D	G3DSA:3.30.70.240	-
2	235	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
2	235	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
2	593	PANTHER	PTHR43512	TRANSLATION FACTOR GUF1-RELATED
2	593	InterPro	IPR006297	Elongation factor 4
399	493	SUPERFAMILY	SSF54980	EF-G C-terminal domain-like
399	493	InterPro	IPR035647	EF-G domain III/V-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_A0A0H3H1L4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00811	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
36				0.546
4				0.011
6				0.001
20				0.0

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	11.92	0.546
2	10.2	0.472
3	8.13	0.367
4	6.09	0.25
5	5.6	0.223

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
31				0.624
2				0.026
28				0.021
19				0.0

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	11.83	0.543
2	10.07	0.466
3	7.73	0.344
4	4.81	0.176
5	4.61	0.164

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.

58 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
5MU	5J8B	Q5SKA7	338.2 Da LogP -2.43 TPSA 171.3	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…`
APR	1U2R	P32324	559.3 Da LogP -3.28 TPSA 291.5	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
G4P	4ZCM	P0A3B2	603.2 Da LogP -2.22 TPSA 345.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
GCP	6U43	A0A062V290	521.2 Da LogP -2.22 TPSA 289.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
GNP	2YWF	O67618	522.2 Da LogP -2.76 TPSA 301.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
MOU	2NPF	P32324	690.8 Da LogP 4.50 TPSA 175.1	1 viol.	✓ Clean	`C[C@@H]1CC[C@@H]2[C@@H]1C[C@@]3([C@@H]4C[C@]2([…`
SO1	1N0U	P32324	494.6 Da LogP 2.49 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@@H]1CC[C@@H]2[C@@H]1C[C@@]3([C@H]4CC([C@@]3…`
SOD	2E1R	P32324	519.1 Da LogP 4.85 TPSA 82.1	1 viol.	✓ Clean	`C[C@@H]1[C@@H](C[C@@H]2[C@@H]1C[C@@]3([C@@H]4C[…`

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
ZINC12360002	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC104869865	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC12501413	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC13518964	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.768	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC105372833	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC31475423	0.738	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=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.