X-group (possible homology)

7570 MurD-like peptide ligases, peptide-binding domain

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Ligands and drugs

1,681

Member domains

131

with ligand contacts (≤ 4 Å)

7.8% of members

113

with DrugDomain annotations

6.7% of members

with a DrugBank compound

5.4% of members

Aggregated over all current member domains of this group. Drug annotations come from DrugDomain; buffers and crystallization additives are excluded from the tables below.

Chemical profile

ClassyFire chemical superclasses of the ligands bound by this X-group's proteins, from DrugDomain annotations.

Proteins with classified ligands

Superclasses bound (of 23)

6.4

Superclasses per 20 proteins

narrower than 69% of the 256 X-groups with enough proteins to compare (median 7.6)

The raw number of superclasses rises with the number of proteins sampled; the per-20 value compares X-groups at equal depth.

Superclass	Proteins	Expected	Ratio	Significance
Nucleosides, nucleotides, and analogues	22	8.5	2.60×	q < 0.0001
Homogeneous metal compounds	16	15.0	1.07×	q = 0.79
Homogeneous non-metal compounds	6	6.6	0.91×	q = 1.00
Organic oxygen compounds	0	6.1	0	q = 5.0e-3
Organosulfur compounds	1	0.6	1.59×	not tested
Organic acids and derivatives	7	4.7	1.48×	not tested
Benzenoids	2	2.2	0.90×	not tested
Organoheterocyclic compounds	2	4.7	0.42×	not tested

enriched (q < 0.05)depleted (q < 0.05)not significantnot tested (expected < 5)

Unit: a protein (UniProt accession) with a ligand-binding domain in this X-group, counted once per superclass. Expected counts use each superclass's frequency across all ligand-binding X-groups; significance is Fisher's exact test with Benjamini–Hochberg correction. Buffers and crystallization additives are excluded. ECOD v295.2; the method follows the ECOD 2027 update, whose published figures used a slightly different artifact filter.

DrugBank compounds

DrugBank	PDB ligand	Name	Domains
DB16833	ADP	Adenosine disphosphate	21
DB00171	ATP	ATP	11
DB01673	UMA	Uridine-5'-Diphosphate-N-Acetylmuramoyl-L-Alanine	6
DB02314	UAG	Uridine-5'-Diphosphate-N-Acetylmuramoyl-L-Alanine-D-Glutamate	6
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	5
DB00130	GLN	L-Glutamine	4
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	4
DB03590	API	2,6-Diaminopimelic Acid	3
DB00131	AMP	Adenosine phosphate	2
DB03345	BME	Mercaptoethanol	2
DB00139	SIN	Succinic acid	1
DB00142	—	Glutamic acid	1
DB00293	—	Raltitrexed	1
DB01762	AAE	Acetoacetic acid	1
DB02301	TMF	5,10-Methylene-6-Hydrofolic Acid	1
DB03755	ACQ	Adenosine-5'-[Beta, Gamma-Methylene]Tetraphosphate	1
DB03830	PD8	Phosphorylated Dihydropteroate	1
DB06813	—	—	1
DB06970	2LG	2-CHLORO-N-(3-CYANO-5,6-DIHYDRO-4H-CYCLOPENTA[B]THIOPHEN-2-YL)-5-DIETHYLSULFAMOYL-BENZAMIDE	1
DB08105	LK1	N-[(6-butoxynaphthalen-2-yl)sulfonyl]-L-glutamic acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ADP	ADENOSINE-5'-DIPHOSPHATE	22
ATP	ADENOSINE-5'-TRIPHOSPHATE	20
MGmetal	MAGNESIUM ION	11
CL	CHLORIDE ION	9
ACP	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER	8
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	7
UMA	URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE	7
AGS	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER	4
ZNmetal	ZINC ION	4
AMP	ADENOSINE MONOPHOSPHATE	3
API	2,6-DIAMINOPIMELIC ACID	3
AZI	AZIDE ION	3
CAmetal	CALCIUM ION	3
A1J52	(1~{R},2~{R})-1-[[4-[(5-~{tert}-butyl-1-methyl-pyrazol-3-yl)amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-6-yl]amino]-2,3-dihydro-1~{H}-inden-2-ol	2
BME	BETA-MERCAPTOETHANOL	2
COmetal	COBALT (II) ION	2
UML	Uridine 5'Diphospho N-acetyl muramoyl-L-Alanyl-D-Glutamyl-L-Lysine	2
051	(1R,3R,4S)-4-[({6-[(4-CYANO-2-FLUOROBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)AMINO]CYCLOHEXANE-1,3-DICARBOXYLIC ACID	1
1LG	2,4-DICHLORO-N-(3-CYANO-4,5,6,7-TETRAHYDRO-BENZOTHIOPHEN-2YL)-5-(MORPHOLINE-4-SULFONYL)-BENZAMIDE	1
2GN	N-(6-(4-(2h-tetrazol-5-yl)benzyl)-3-cyano-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl)-2,4-dichloro-5-(morpholinosulfonyl)benzamide	1