Protein profile

KP13_01908

Phospho-N-acetylmuramoyl-pentapeptide- transferase

Genome: KpKP13

Gene: AHE46349.1 mraY Structure source: AlphaFold + ColabFold UniProt A0A0H3GI63

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Amino acids 360

Annotations 11

Features 46

PDB binders 2

Druggability 0.685

Overview

Basic information about this protein and its source genome.

Accession: KP13_01908
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46349.1 mraY
Status: annotated
Amino acids: 360
Structure source: AlphaFold + ColabFold

2.7.8.13

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0008963 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine = Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UMP. GO:0016780 Catalysis of the transfer of a substituted phosphate group, other than diphosphate or nucleotidyl residues, from one compound (donor) to a another (acceptor). 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:0046872 Binding to a metal ion. GO:0051992 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP.

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 (%): 98.056
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 91.95

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 0.685

Structure A0A0H3GI63

Pocket Pocket 2

P2Rank 0.848

Structure A0A0H3GI63

Pocket Pocket 1

ColabFold model

FPocket 0.857 · Pocket 3

P2Rank 0.818 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 320 / 4744 genomes with a hit

Normalized 0.067

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

2.7.8.13

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0008963 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine = Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UMP.
GO:0016780 Catalysis of the transfer of a substituted phosphate group, other than diphosphate or nucleotidyl residues, from one compound (donor) to a another (acceptor).
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:0046872 Binding to a metal ion.
GO:0051992 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP.
GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

46 records

Show feature table

Start	End	DB	Term	Name
358	360	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
234	256	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
285	289	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
61	356	CDD	cd06852	GT_MraY
61	356	InterPro	IPR003524	Phospho-N-acetylmuramoyl-pentapeptide transferase
1	19	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
68	80	Pfam	PF10555	Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
68	80	InterPro	IPR018480	Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site
20	40	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
25	358	Hamap	MF_00038	Phospho-N-acetylmuramoyl-pentapeptide-transferase [mraY].
25	358	InterPro	IPR003524	Phospho-N-acetylmuramoyl-pentapeptide transferase
200	219	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
68	80	ProSitePatterns	PS01347	MraY family signature 1.
338	357	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
115	133	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20	42	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
99	284	Pfam	PF00953	Glycosyl transferase family 4
99	284	InterPro	IPR000715	Glycosyl transferase, family 4
41	72	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
263	285	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
194	199	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
134	152	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
200	219	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
134	151	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
257	262	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
220	238	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
97	114	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
37	360	NCBIfam	TIGR00445	phospho-N-acetylmuramoyl-pentapeptide-transferase
37	360	InterPro	IPR003524	Phospho-N-acetylmuramoyl-pentapeptide transferase
312	337	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
289	311	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
23	358	PANTHER	PTHR22926	PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE
23	358	InterPro	IPR000715	Glycosyl transferase, family 4
239	256	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
96	114	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
153	171	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
290	311	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
75	92	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
172	193	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
73	90	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
171	193	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
263	284	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
189	200	ProSitePatterns	PS01348	MraY family signature 2.
189	200	InterPro	IPR018480	Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site
91	95	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
338	357	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GI63	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01908	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
2				0.685
5				0.41
3				0.363

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	13.65	0.694
2	3.25	0.113
3	2.22	0.054
4	2.17	0.051
5	1.77	0.033

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
3				0.857

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	13.33	0.682
2	4.58	0.197
3	3.18	0.109
4	1.85	0.036
5	1.34	0.015

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.

37 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
NK4	6OYH	O66465	798.0 Da LogP 1.05 TPSA 250.3	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCC[C@H]1CN([C@H](C(=O)N([C@@H]1C…`
NKD	6OZ6	O66465	856.9 Da LogP -1.83 TPSA 328.0	3 viol.	✓ Clean	`C[C@@H]([C@@H](C(=O)N/C=C\1/[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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL4286766	P0C1R8	10.80	946.0 Da LogP -6.69 TPSA 432.6	3 viol.	✓ Clean	`CO[C@H]1[C@H](O[C@H]([C@H]2O[C@@H](n3ccc(=O)[nH…`
CHEMBL4284923	P0C1R8	10.03	988.0 Da LogP -6.51 TPSA 435.7	3 viol.	✓ Clean	`CO[C@H]1[C@H](O[C@H]([C@H]2O[C@@H](n3ccc(=O)[nH…`
CHEMBL4279378	O66465	9.49	1156.3 Da LogP -1.58 TPSA 438.7	3 viol.	✓ Clean	`CO[C@H]1[C@H](O[C@H]([C@H]2O[C@@H](n3ccc(=O)[nH…`
CHEMBL4475677	P0C1R8	8.59	784.0 Da LogP 0.71 TPSA 259.1	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCC[C@@H]1CN[C@@H]([C@H](O[C@@H]2…`
57M	Q03521	8.12	916.0 Da LogP -6.52 TPSA 425.9	3 viol.	✓ Clean	`CC(C)C[C@@H](C(=O)NCCCN[C@@H]([C@@H]([C@@H]1[C@…`
CHEMBL5282738	E2QF15	8.00	649.7 Da LogP -3.07 TPSA 242.8	3 viol.	✓ Clean	`CO[C@H]1[C@@H](OC)[C@H](n2ccc(=O)[nH]c2=O)O[C@@…`
CHEMBL4283943	P9WMW7	7.96	930.0 Da LogP -5.66 TPSA 412.4	3 viol.	✓ Clean	`CO[C@H]1[C@H](O[C@H]([C@H]2O[C@@H](n3ccc(=O)[nH…`
CHEMBL5265940	P0C1R8	7.77	583.6 Da LogP -4.18 TPSA 253.8	3 viol.	✓ Clean	`CO[C@H]1[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O[C@@H…`
CHEMBL95027	P0A6W3	7.77	583.6 Da LogP -4.18 TPSA 253.8	3 viol.	✓ Clean	`CO[C@H]1[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O[C@@H…`
NKM	P0A6W3	7.75	569.5 Da LogP -4.57 TPSA 253.8	3 viol.	✓ Clean	`CO[C@H]1[C@H]([C@@H](O[C@@H]1[C@H](C(=O)N)O[C@@…`
CHEMBL2048825	P0C1R8	7.66	711.7 Da LogP -1.68 TPSA 283.1	3 viol.	✓ Clean	`C[C@H](N)C(=O)N(C)[C@@H](C)[C@H](NC(=O)[C@H](C)…`
CHEMBL2048828	P0C1R8	7.66	876.9 Da LogP -2.67 TPSA 352.6	3 viol.	✓ Clean	`C[C@H](NC(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O)C…`
CHEMBL5272467	Q03521	7.66	726.7 Da LogP -2.74 TPSA 309.1	3 viol.	✓ Clean	`C[C@@H](NC(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O)…`
CHEMBL4473600	P0C1R8	7.62	711.9 Da LogP 0.66 TPSA 230.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N[C@H]1CCN[C@H]([C@H](O[C@@…`
CHEMBL5277590	P0C1R8	7.57	473.4 Da LogP -4.18 TPSA 221.9	1 viol.	✓ Clean	`COC(=O)C1=C[C@@H](O)[C@@H](O)[C@H](O[C@@H](C(N)…`
CHEMBL2048826	P0C1R8	7.38	727.7 Da LogP -2.71 TPSA 303.3	3 viol.	✓ Clean	`C[C@H](N)C(=O)N(C)[C@@H](C)[C@H](NC(=O)[C@H](C)…`
CHEMBL5271984	Q03521	7.38	713.7 Da LogP -3.05 TPSA 312.1	3 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@@H](C)[C@H](NC(=O)[C@H](C)NC(…`
CHEMBL1780217	Q03521	7.31	916.0 Da LogP -6.31 TPSA 423.4	3 viol.	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@@H](NC(=O)N[C@H](C(=O)O)C…`
CHEMBL5278937	E2QF15	7.24	601.6 Da LogP -4.62 TPSA 253.8	3 viol.	✓ Clean	`CO[C@H]1[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O[C@@H…`
CHEMBL2048830	P0C1R8	7.19	713.7 Da LogP -3.10 TPSA 303.3	3 viol.	✓ Clean	`C[C@H](NC(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O)C…`
CHEMBL1780218	Q03521	6.61	1070.3 Da LogP -1.88 TPSA 423.4	3 viol.	✓ Clean	`CCCCCCCCCCCCCCC[C@H](NC(=O)[C@@H](NC(=O)N[C@H](…`
9LH	P0C1R8	6.60	830.9 Da LogP -2.48 TPSA 311.8	3 viol.	✓ Clean	`CC(C)CCCCCCCCC/C=C/C(=O)N[C@@H]1[C@H]([C@H]([C@…`
CHEMBL5279603	P0C1R8	6.52	490.5 Da LogP -3.42 TPSA 215.5	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H](C#Cc2ccc(N)cc2)[C@H]2O[…`
CHEMBL5267618	P0A6W3	6.48	502.6 Da LogP -2.49 TPSA 201.5	3 viol.	✓ Clean	`CCCCCCCNCC(O[C@@H]1O[C@H](CN)[C@@H](O)[C@H]1O)[…`
CHEMBL5275061	P0A6W3	6.48	586.7 Da LogP -0.15 TPSA 201.5	3 viol.	✓ Clean	`CCCCCCCCCCCCCNCC(O[C@@H]1O[C@H](CN)[C@@H](O)[C@…`
CHEMBL5276993	P0A6W3	6.48	558.7 Da LogP -0.93 TPSA 201.5	3 viol.	✓ Clean	`CCCCCCCCCCCNCC(O[C@@H]1O[C@H](CN)[C@@H](O)[C@H]…`
CHEMBL5281271	P0A6W3	6.48	460.5 Da LogP -3.66 TPSA 201.5	2 viol.	✓ Clean	`CCCCNCC(O[C@@H]1O[C@H](CN)[C@@H](O)[C@H]1O)[C@H…`
CHEMBL5288850	P0A6W3	6.48	530.6 Da LogP -1.71 TPSA 201.5	3 viol.	✓ Clean	`CCCCCCCCCNCC(O[C@@H]1O[C@H](CN)[C@@H](O)[C@H]1O…`
CHEMBL5289885	P0C1R8	6.23	551.6 Da LogP -1.33 TPSA 189.5	3 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H](C#Cc2ccc(-c3ccccc3)cc2)…`
CHEMBL2048831	P0C1R8	6.19	876.9 Da LogP -2.67 TPSA 352.6	3 viol.	✓ Clean	`C[C@H](NC(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O)C…`
CHEMBL5277496	P0C1R8	6.19	551.6 Da LogP -1.33 TPSA 189.5	3 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H](C#Cc2cccc(-c3ccccc3)c2)…`
CHEMBL1780219	Q03521	6.16	1070.3 Da LogP -1.88 TPSA 423.4	3 viol.	✓ Clean	`CCCCCCCCCCCCCCC[C@@H](NC(=O)[C@@H](NC(=O)N[C@H]…`
CHEMBL5287014	P0C1R8	6.05	594.6 Da LogP -1.75 TPSA 218.6	3 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H](C#Cc2ccc(C(=O)Nc3ccccc3…`
CHEMBL5268197	P0C1R8	6.02	630.6 Da LogP -2.20 TPSA 235.7	3 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H](C#Cc2cccc(NS(=O)(=O)c3c…`
CHEMBL5291217	P0C1R8	6.00	630.6 Da LogP -2.20 TPSA 235.7	3 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H](C#Cc2ccc(NS(=O)(=O)c3cc…`

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

No virtual-screening candidates for this protein.

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.