X-group (possible homology)

5033 Photosystem II reaction center protein M, PsbM

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Ligands and drugs

383

Member domains

335

with ligand contacts (≤ 4 Å)

87.5% of members

221

with DrugDomain annotations

57.7% of members

191

with a DrugBank compound

49.9% 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)

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Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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
Homogeneous metal compounds	1	6.3	0.16×	q = 7.6e-3
Hydrocarbons	1	0.1	11×	not tested
Lipids and lipid-like molecules	13	1.4	9.11×	not tested
Organoheterocyclic compounds	1	2.0	0.51×	not tested
Organic acids and derivatives	1	2.0	0.50×	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
DB02043	LHG	1,2-Dipalmitoyl-Phosphatidyl-Glycerole	181
DB03193	STE	Stearic acid	50
DB02133	CLA	Chlorophyll A	13
DB03426	DGD	Digalactosyl Diacyl Glycerol (Dgdg)	13
DB04735	MGE	Monogalactosyldiacylglycerol	8
DB06755	BCR	Beta carotene	4
DB04464	FME	N-Formylmethionine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CLA	CHLOROPHYLL A	327
LMG	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	317
BCR	BETA-CAROTENE	306
LHG	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	291
SQD	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	267
UNL	Unknown ligand	97
STE	STEARIC ACID	54
DGD	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	15
8CT	(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene	11
MGE	(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE	10
3PH	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE	9
CL7	CHLOROPHYLL D	6
WVN	1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene	4
LFA	EICOSANE	3
PLM	PALMITIC ACID	3
LNL	ALPHA-LINOLENIC ACID	2
FME	N-FORMYLMETHIONINE	1