Protein profile

PA4417

UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase

Genome: NC_002516.2

Gene: PA4417 murE Structure source: AlphaFold UniProt Q59650

Export view

Amino acids 487

Annotations 12

Features 22

PDB binders 14

Druggability 0.475

Overview

Basic information about this protein and its source genome.

Accession: PA4417
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4417 murE
Status: annotated
Amino acids: 487
Structure source: AlphaFold

6.3.2.13

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000287 Binding to a magnesium (Mg) ion. GO:0008765 Catalysis of the reaction: meso-2,6-diaminopimelate + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.475

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

6.3.2.13

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0008765 Catalysis of the reaction: meso-2,6-diaminopimelate + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate.
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.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0016881 Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
11	95	SUPERFAMILY	SSF63418	MurE/MurF N-terminal domain
11	95	InterPro	IPR035911	MurE/MurF, N-terminal
329	412	Pfam	PF02875	Mur ligase family, glutamate ligase domain
329	412	InterPro	IPR004101	Mur ligase, C-terminal
18	94	Pfam	PF01225	Mur ligase family, catalytic domain
18	94	InterPro	IPR000713	Mur ligase, N-terminal catalytic domain
97	326	SUPERFAMILY	SSF53623	MurD-like peptide ligases, catalytic domain
97	326	InterPro	IPR036565	Mur-like, catalytic domain superfamily
17	479	NCBIfam	TIGR01085	UDP-N-acetylmuramyl-tripeptide synthetase
17	479	InterPro	IPR005761	UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase
330	483	Gene3D	G3DSA:3.90.190.20	-
330	483	InterPro	IPR036615	Mur ligase, C-terminal domain superfamily
3	479	Hamap	MF_00208	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase [murE].
3	479	InterPro	IPR005761	UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase
97	329	Gene3D	G3DSA:3.40.1190.10	-
97	329	InterPro	IPR036565	Mur-like, catalytic domain superfamily
106	306	Pfam	PF08245	Mur ligase middle domain
106	306	InterPro	IPR013221	Mur ligase, central
3	96	Gene3D	G3DSA:3.40.1390.10	-
3	482	PANTHER	PTHR23135	MUR LIGASE FAMILY MEMBER
329	480	SUPERFAMILY	SSF53244	MurD-like peptide ligases, peptide-binding domain
329	480	InterPro	IPR036615	Mur ligase, C-terminal domain 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...

Legend High Medium Low

Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA4417	AlphaFold	—	—	full sequence	—	Viewing

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
1				0.475

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.

64 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
ACP	4CVL	Q9HVZ7	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	4ZIY	A0A0D5YEC3	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
API	1E8C	P22188	190.2 Da LogP -1.02 TPSA 126.6	✓ Ro5	✓ Clean	`C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N`
JHP	7B9E	P22188	227.7 Da LogP 1.75 TPSA 46.9	✓ Ro5	✓ Clean	`Cn1cc(c(n1)C(=O)NC2CCCC2)Cl`
LVV	7B68	P22188	239.3 Da LogP 1.23 TPSA 37.4	✓ Ro5	✓ Clean	`Cc1ccc(cc1)CN2CCS(=O)(=O)CC2`
O3D	7B60	P22188	215.3 Da LogP 0.51 TPSA 50.5	✓ Ro5	✓ Clean	`c1cc(oc1)CN2CCS(=O)(=O)CC2`
SYQ	7B61	P22188	204.3 Da LogP 1.92 TPSA 42.0	✓ Ro5	✓ Clean	`Cc1cccc(n1)C(=O)N[C@@H](C)C2CC2`
SYZ	7B6N	P22188	278.3 Da LogP 1.42 TPSA 66.5	✓ Ro5	✓ Clean	`Cc1cccc(c1)C(=O)NCCN2C(=O)CSC2=O`
SZK	7B6L	P22188	241.3 Da LogP 3.26 TPSA 43.0	✓ Ro5	✓ Clean	`CCn1c2ccccc2nc1NCc3ccco3`
SZN	7B6M	P22188	260.3 Da LogP 0.87 TPSA 66.5	✓ Ro5	✓ Clean	`Cc1cccc(c1)C(=O)NCCN2C(=O)CCC2=O`
T3Z	7B61	P22188	204.3 Da LogP 1.92 TPSA 42.0	✓ Ro5	✓ Clean	`Cc1cccc(n1)C(=O)N[C@H](C)C2CC2`
UAG	1E8C	P22188	879.6 Da LogP -5.30 TPSA 427.7	3 viol.	✓ Clean	`C[C@@H](C(=O)N[C@H](CCC(=O)O)C(=O)O)NC(=O)[C@@H…`
UML	4C12	Q2FZP6	1007.8 Da LogP -5.68 TPSA 482.8	3 viol.	✓ Clean	`C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCCCN)C(=O)O…`
WZD	7B6Q	P22188	213.2 Da LogP 2.77 TPSA 53.9	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c(n2)NCc3ccco3`

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
ZINC19851827	1.000	215.3 Da LogP 0.51 TPSA 50.5	✓ Ro5	✓ Clean	`O=S1(=O)CCN(Cc2ccco2)CC1`
ZINC25773506	1.000	204.3 Da LogP 1.92 TPSA 42.0	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)N[C@H](C)C2CC2)n1`
ZINC25773508	1.000	204.3 Da LogP 1.92 TPSA 42.0	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)N[C@@H](C)C2CC2)n1`
ZINC467615	1.000	227.7 Da LogP 1.75 TPSA 46.9	✓ Ro5	✓ Clean	`Cn1cc(Cl)c(C(=O)NC2CCCC2)n1`
ZINC47693073	1.000	278.3 Da LogP 1.42 TPSA 66.5	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)NCCN2C(=O)CSC2=O)c1`
ZINC513005	1.000	213.2 Da LogP 2.77 TPSA 53.9	✓ Ro5	✓ Clean	`c1coc(CNc2nc3ccccc3[nH]2)c1`
ZINC513479	1.000	241.3 Da LogP 3.26 TPSA 43.0	✓ Ro5	✓ Clean	`CCn1c(NCc2ccco2)nc2ccccc21`
ZINC59601259	1.000	239.3 Da LogP 1.23 TPSA 37.4	✓ Ro5	✓ Clean	`Cc1ccc(CN2CCS(=O)(=O)CC2)cc1`
ZINC72818936	1.000	260.3 Da LogP 0.87 TPSA 66.5	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)NCCN2C(=O)CCC2=O)c1`
ZINC2487640	0.971	241.7 Da LogP 2.14 TPSA 46.9	✓ Ro5	✓ Clean	`Cn1cc(Cl)c(C(=O)NC2CCCCC2)n1`
ZINC468315	0.971	255.7 Da LogP 2.53 TPSA 46.9	✓ Ro5	✓ Clean	`Cn1cc(Cl)c(C(=O)NC2CCCCCC2)n1`
ZINC3055005	0.882	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.882	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.882	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC105469665	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC13527614	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC219330894	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873852	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873853	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC3873854	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873855	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC12360002	0.839	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	0.839	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	0.839	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	0.839	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	0.839	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	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.839	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	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.839	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	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC1555366	0.833	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.833	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.833	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127	0.833	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.833	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.833	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC513251	0.814	255.3 Da LogP 3.65 TPSA 43.0	✓ Ro5	✓ Clean	`CCCn1c(NCc2ccco2)nc2ccccc21`
ZINC16546165	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC13518964	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.768	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	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC2046931	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201893	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.768	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	0.768	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	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](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.