X-group (possible homology)

2007 Flavodoxin-like

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Ligands and drugs

67,130

Member domains

15,563

with ligand contacts (≤ 4 Å)

23.2% of members

12,989

with DrugDomain annotations

19.3% of members

8,518

with a DrugBank compound

12.7% 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.

1,212

Proteins with classified ligands

Superclasses bound (of 23)

8.9

Superclasses per 20 proteins

broader than 77% 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
Mixed metal/non-metal compounds	74	25.1	2.95×	q < 0.0001
Organic oxygen compounds	335	238.0	1.41×	q < 0.0001
Homogeneous non-metal compounds	321	257.2	1.25×	q < 0.0001
Organic acids and derivatives	221	184.9	1.20×	q = 8.4e-3
Organosulfur compounds	25	24.6	1.02×	q = 0.95
Nucleosides, nucleotides, and analogues	304	330.3	0.92×	q = 0.13
Homogeneous metal compounds	496	586.6	0.85×	q < 0.0001
Benzenoids	72	87.4	0.82×	q = 0.14
Organic nitrogen compounds	29	38.1	0.76×	q = 0.19
Organoheterocyclic compounds	114	183.9	0.62×	q < 0.0001
Lipids and lipid-like molecules	60	133.1	0.45×	q < 0.0001
Phenylpropanoids and polyketides	11	24.9	0.44×	q = 5.9e-3
Hydrocarbons	0	8.4	0	q = 8.9e-4
Organophosphorus compounds	1	0.4	2.47×	not tested
Miscellaneous inorganic compounds	1	0.9	1.12×	not tested
Organometallic compounds	1	1.7	0.59×	not tested
Organohalogen compounds	1	3.4	0.29×	not tested
Alkaloids and derivatives	1	4.1	0.24×	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
DB00141	NAG	N-Acetylglucosamine	868
DB03247	FMN	Flavin mononucleotide	538
DB03147	FAD	Flavin adenine dinucleotide	256
DB14128	NAD	Nadide	227
DB00142	GLU	Glutamic acid	180
DB02338	NDP	NADPH	174
DB01992	COA	Coenzyme A	147
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	135
DB00171	ATP	ATP	127
DB02517	DGL	D-Glutamic Acid	108
DB02379	BGC	Beta-D-Glucose	97
DB03581	G6Q	Glucose-6-Phosphate	95
DB16833	ADP	Adenosine disphosphate	86
DB00157	NAI	NADH	83
DB09459	TLA	L-tartaric acid	81
DB00130	GLN	L-Glutamine	78
DB02548	S6P	D-glucitol 6-phosphate	73
DB04162	INI	5-Nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione	70
DB18267	HEM	Ferroheme	66
DB02659	CHD	Cholic Acid	61

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	1,390
MGmetal	MAGNESIUM ION	1,139
CL	CHLORIDE ION	1,132
CAmetal	CALCIUM ION	830
SF4	IRON/SULFUR CLUSTER	778
ZNmetal	ZINC ION	682
FMN	FLAVIN MONONUCLEOTIDE	561
ICS	iron-sulfur-molybdenum cluster with interstitial carbon	462
HCA	3-HYDROXY-3-CARBOXY-ADIPIC ACID	458
NAmetal	SODIUM ION	404
FEmetal	FE (III) ION	391
CLF	FE(8)-S(7) CLUSTER	382
MNmetal	MANGANESE (II) ION	329
FAD	FLAVIN-ADENINE DINUCLEOTIDE	278
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	262
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	258
B12	COBALAMIN	205
BEF	BERYLLIUM TRIFLUORIDE ION	158
Kmetal	POTASSIUM ION	152
COA	COENZYME A	148