Protein profile

VK055_5027

mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Genome: KpATCC43816

Gene: AIK83553.1 manC Structure source: AlphaFold + ColabFold UniProt Q48462

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Amino acids 471

Annotations 9

Features 19

PDB binders 1

Druggability 0.103

Overview

Basic information about this protein and its source genome.

Accession: VK055_5027
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83553.1 manC
Status: annotated
Amino acids: 471
Structure source: AlphaFold + ColabFold

2.7.7.13

GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GO:0005976 The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor). 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. GO:0005525 Binding to GTP, guanosine triphosphate. GO:0004475 Catalysis of the reaction: alpha-D-mannose 1-phosphate + GTP = diphosphate + GDP-alpha-D-mannose.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 58.298
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.84

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 0.103

Structure Q48462

Pocket Pocket 1

P2Rank 0.923

Structure Q48462

Pocket Pocket 1

ColabFold model

FPocket 0.097 · Pocket 6

P2Rank 0.931 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 108 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

2.7.7.13

Gene Ontology (GO)

GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GO:0005976 The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
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.
GO:0005525 Binding to GTP, guanosine triphosphate.
GO:0004475 Catalysis of the reaction: alpha-D-mannose 1-phosphate + GTP = diphosphate + GDP-alpha-D-mannose.
GO:0009298 The chemical reactions and pathways resulting in the formation of GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
2	282	SUPERFAMILY	SSF53448	Nucleotide-diphospho-sugar transferases
2	282	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
349	470	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
349	470	InterPro	IPR014710	RmlC-like jelly roll fold
2	351	FunFam	G3DSA:3.90.550.10:FF:000046	Mannose-1-phosphate guanylyltransferase (GDP)
2	464	PANTHER	PTHR46390	MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
316	466	Pfam	PF01050	Mannose-6-phosphate isomerase
316	466	InterPro	IPR001538	Mannose-6-phosphate isomerase, type II, C-terminal
2	348	Gene3D	G3DSA:3.90.550.10	Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
2	348	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
2	470	NCBIfam	TIGR01479	mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
2	470	InterPro	IPR006375	Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
348	465	FunFam	G3DSA:2.60.120.10:FF:000032	Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
337	464	CDD	cd02213	cupin_PMI_typeII_C
186	470	SUPERFAMILY	SSF51182	RmlC-like cupins
186	470	InterPro	IPR011051	RmlC-like cupin domain superfamily
4	279	CDD	cd02509	GDP-M1P_Guanylyltransferase
4	288	Pfam	PF00483	Nucleotidyl transferase
4	288	InterPro	IPR005835	Nucleotidyl transferase domain

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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_Q48462	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_5027	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	18.78	0.83
2	16.18	0.772
3	8.3	0.442
4	2.94	0.094
5	1.77	0.033

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	14.02	0.708
2	13.25	0.679
3	8.39	0.447
4	5.45	0.259
5	1.93	0.04

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.

51 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
GDD	2X5Z	Q9X0C3	605.3 Da LogP -4.63 TPSA 331.7	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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
ZINC104869865	0.761	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	0.761	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	0.761	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	0.761	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	0.761	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	0.761	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	0.761	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	0.701	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	0.701	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	0.701	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	0.701	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	0.701	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	0.701	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	0.701	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	0.701	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	0.701	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)[…`
ZINC1532637	0.672	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…`
ZINC1550030	0.672	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…`
ZINC1570863	0.672	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(…`
ZINC1698205	0.672	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	0.672	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(…`
ZINC3869967	0.672	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…`
ZINC3869968	0.672	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)…`
ZINC3869969	0.672	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)…`
ZINC3869970	0.672	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…`
ZINC5605239	0.672	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…`
ZINC6119283	0.672	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	0.672	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	0.672	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…`
ZINC100727895	0.662	347.2 Da LogP -2.50 TPSA 196.8	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2P(=…`
ZINC17610743	0.662	347.2 Da LogP -2.50 TPSA 196.8	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2P(…`
ZINC12501360	0.648	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2OP…`
ZINC12503440	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC1530370	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC28631009	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC3872740	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872741	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC3872742	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872743	0.634	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC71774763	0.618	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	0.597	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	0.597	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	0.597	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	0.597	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…`
ZINC106042635	0.595	341.3 Da LogP -2.02 TPSA 157.7	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=…`
ZINC230402607	0.595	341.3 Da LogP -2.02 TPSA 157.7	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@@H](O)[C@@H](CO)O[C@@H]1n1cnc2c(…`
ZINC230402611	0.595	341.3 Da LogP -2.02 TPSA 157.7	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@@H](n2cnc3c(=O)[nH]c(N)nc32)O[C@…`
ZINC2583384	0.595	341.3 Da LogP -2.02 TPSA 157.7	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1cnc2c(=O…`
ZINC85475068	0.595	341.3 Da LogP -2.02 TPSA 157.7	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](n2cnc3c(=O)[nH]c(N)nc32)O[C@H…`
ZINC90556174	0.595	341.3 Da LogP -2.02 TPSA 157.7	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](O)[C@@H](CO)O[C@@H]1n1cnc2c(=…`

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.