Protein profile

KP13_01100

Translation initiation factor IF-2

Genome: KpKP13

Gene: AHE42508.1 infB Structure source: AlphaFold + ColabFold UniProt A0A0H3GY08

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Amino acids 896

Annotations 6

Features 54

PDB binders 11

Druggability 0.644

Overview

Basic information about this protein and its source genome.

Accession: KP13_01100
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42508.1 infB
Status: annotated
Amino acids: 896
Structure source: AlphaFold + ColabFold

GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate. GO:0005525 Binding to GTP, guanosine triphosphate. GO:0003743 Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide. GO:0006413 The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0097216 Binding to guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 41.468
Human E-value: 5.97e-126
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 93.631
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 79.13

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 0.644

Structure A0A0H3GY08

Pocket Pocket 4

P2Rank 0.091

Structure A0A0H3GY08

Pocket Pocket 1

ColabFold model

FPocket 0.463 · Pocket 46

P2Rank 0.244 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 153 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
GO:0005525 Binding to GTP, guanosine triphosphate.
GO:0003743 Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
GO:0006413 The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0097216 Binding to guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records

Show feature table

Start	End	DB	Term	Name
93	304	MobiDBLite	mobidb-lite	consensus disorder prediction
802	885	CDD	cd03692	mtIF2_IVc
312	895	NCBIfam	TIGR00487	translation initiation factor IF-2
312	895	InterPro	IPR000178	Translation initiation factor IF-2, bacterial-like
400	556	Pfam	PF00009	Elongation factor Tu GTP binding domain
400	556	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
238	259	MobiDBLite	mobidb-lite	consensus disorder prediction
2	50	FunFam	G3DSA:3.30.56.50:FF:000001	Translation initiation factor IF-2
393	566	Gene3D	G3DSA:3.40.50.300	-
393	566	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
2	50	Gene3D	G3DSA:3.30.56.50	-
57	95	Pfam	PF08364	Bacterial translation initiation factor IF-2 associated region
57	95	InterPro	IPR013575	Initiation factor 2 associated domain, bacterial
671	785	Pfam	PF11987	Translation-initiation factor 2
671	785	InterPro	IPR023115	Translation initiation factor IF- 2, domain 3
100	155	Coils	Coil	Coil
268	289	MobiDBLite	mobidb-lite	consensus disorder prediction
690	796	FunFam	G3DSA:3.40.50.10050:FF:000001	Translation initiation factor IF-2
398	561	CDD	cd01887	IF2_eIF5B
567	685	FunFam	G3DSA:2.40.30.10:FF:000007	Translation initiation factor IF-2
399	554	NCBIfam	TIGR00231	small GTP-binding protein domain
399	554	InterPro	IPR005225	Small GTP-binding protein domain
571	664	CDD	cd03702	IF2_mtIF2_II
571	664	InterPro	IPR044145	Translation initiation factor IF-2, domain II
797	894	FunFam	G3DSA:2.40.30.10:FF:000008	Translation initiation factor IF-2
395	564	ProSiteProfiles	PS51722	Translational (tr)-type guanine nucleotide-binding (G) domain profile.
395	564	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
395	563	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
395	563	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
567	685	Gene3D	G3DSA:2.40.30.10	Translation factors
3	893	Hamap	MF_00100_B	Translation initiation factor IF-2 [infB].
3	893	InterPro	IPR000178	Translation initiation factor IF-2, bacterial-like
690	796	Gene3D	G3DSA:3.40.50.10050	-
690	796	InterPro	IPR036925	Translation initiation factor IF-2, domain 3 superfamily
105	894	PANTHER	PTHR43381	TRANSLATION INITIATION FACTOR IF-2-RELATED
105	894	InterPro	IPR015760	Translation initiation factor IF- 2
568	650	SUPERFAMILY	SSF50447	Translation proteins
568	650	InterPro	IPR009000	Translation protein, beta-barrel domain superfamily
168	218	Coils	Coil	Coil
846	868	ProSitePatterns	PS01176	Initiation factor 2 signature.
846	868	InterPro	IPR000178	Translation initiation factor IF-2, bacterial-like
797	894	Gene3D	G3DSA:2.40.30.10	Translation factors
1	52	Pfam	PF04760	Translation initiation factor IF-2, N-terminal region
1	52	InterPro	IPR006847	Translation initiation factor IF-2, N-terminal
320	370	Pfam	PF04760	Translation initiation factor IF-2, N-terminal region
320	370	InterPro	IPR006847	Translation initiation factor IF-2, N-terminal
3	50	SUPERFAMILY	SSF46955	Putative DNA-binding domain
3	50	InterPro	IPR009061	Putative DNA-binding domain superfamily
392	566	FunFam	G3DSA:3.40.50.300:FF:000019	Translation initiation factor IF-2
797	893	SUPERFAMILY	SSF50447	Translation proteins
797	893	InterPro	IPR009000	Translation protein, beta-barrel domain superfamily
93	228	MobiDBLite	mobidb-lite	consensus disorder prediction
673	802	SUPERFAMILY	SSF52156	Initiation factor IF2/eIF5b, domain 3
673	802	InterPro	IPR036925	Translation initiation factor IF-2, domain 3 superfamily

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_A0A0H3GY08	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01100	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
4				0.644
1				0.319

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	1.95	0.04
2	1.92	0.039
3	1.33	0.015
4	1.28	0.013
5	0.92	0.004

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
46				0.463
18				0.255
70				0.241

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	2.28	0.057
2	2.01	0.044
3	1.4	0.017
4	1.31	0.014
5	1.14	0.009

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.

61 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
5GP	6GAW	P46199	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
DTT	4TMT	G0S8G9	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
FES	6RW5	P46199	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
FME	3JCJ	P0A705	177.2 Da LogP -0.06 TPSA 66.4	✓ Ro5	✓ Clean	`CSCC[C@@H](C(=O)O)NC=O`
GCP	4V8Y	P39730	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	3JCJ	P0A705	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…`
GSP	6GAW	P46199	539.2 Da LogP -2.22 TPSA 282.0	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
LAC	4N3N	G0S8G9	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
OHX	4V8Y	P39730	286.4 Da LogP -3.55 TPSA 156.1	1 viol.	✓ Clean	`N[Os](N)(N)(N)(N)N`
SPM	6GAW	P46199	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CNCCCN`
SRY	6RW5	P46199	581.6 Da LogP -7.74 TPSA 331.4	3 viol.	✓ Clean	`[H]/N=C(/N)\N[C@@H]1[C@H]([C@@H]([C@H]([C@@H]([…`

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
ZINC1532734	1.000	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNCCCCNCCCN`
ZINC27564039	0.867	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCNCCCN`
ZINC13377742	0.857	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC104869865	0.836	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	0.836	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	0.836	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	0.836	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	0.836	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	0.836	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	0.836	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)(…`
ZINC1598087	0.800	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC221146246	0.781	308.4 Da LogP 0.18 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](CCSC)NC=O)C(=O)O`
ZINC12501413	0.770	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	0.770	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	0.770	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	0.770	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	0.770	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	0.770	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	0.770	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	0.770	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	0.770	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)[…`
ZINC4544549	0.758	439.6 Da LogP 0.41 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](CCSC)NC(=O)[C@H](CCSC)NC=…`
ZINC2116511	0.686	248.3 Da LogP -0.56 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](C)C(=O)O`
ZINC100056474	0.684	270.5 Da LogP 4.63 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNCCCN`
ZINC59496006	0.684	242.5 Da LogP 3.85 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNCCCN`
ZINC71774763	0.671	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC4743771	0.652	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743772	0.652	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC4743774	0.652	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743775	0.652	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC1576667	0.649	276.4 Da LogP 0.08 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC1674993	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@H](N)C(=O)O)C(=O)O`
ZINC1674994	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1674996	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC12503703	0.638	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…`
ZINC8215878	0.638	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…`
ZINC100058967	0.632	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@H](CO[P@](=O)(O)OP(=O)…`
ZINC12504287	0.632	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC12504288	0.632	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC31308647	0.632	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC1570863	0.629	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(…`
ZINC2020098	0.629	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC38580950	0.629	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC3869968	0.629	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)…`
ZINC4990799	0.629	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC4990802	0.629	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H]…`
ZINC5605239	0.629	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c…`
ZINC6585367	0.629	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC8613125	0.629	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC97973760	0.629	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H](…`

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.