X-group (possible homology)

4004 NAD kinase beta sandwich domain-like

Open in classification tree →

Ligands and drugs

1,255

Member domains

193

with ligand contacts (≤ 4 Å)

15.4% of members

166

with DrugDomain annotations

13.2% of members

116

with a DrugBank compound

9.2% 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)

—

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	6	5.8	1.03×	q = 1.00
Organic nitrogen compounds	1	0.4	2.65×	not tested
Nucleosides, nucleotides, and analogues	8	3.3	2.45×	not tested
Homogeneous non-metal compounds	3	2.6	1.18×	not tested
Benzenoids	1	0.9	1.16×	not tested
Organoheterocyclic compounds	1	1.8	0.55×	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
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	12
DB14128	NAD	Nadide	8
DB00171	ATP	ATP	4
DB16833	ADP	Adenosine disphosphate	3
DB00157	NAI	NADH	2
DB02282	MTA	5'-S-methyl-5'-thioadenosine	2
DB03203	SQS	Sphingosine	2
DB00144	—	Phosphatidyl serine	1
DB12764	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	22
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	12
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	12
UUL	4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol	12
5A8	5'-azido-5'-deoxy-8-[(2-{[2-(1H-indol-3-yl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine	4
5A9	5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine	4
5AG	5'-azido-5'-deoxy-8-[(2-{[2-(3-ethynylphenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine	4
5AJ	5'-azido-8-[(2-{[2-(1H-benzimidazol-2-yl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine	4
5AK	8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine	4
5AQ	8-({2-oxo-2-[(2-phenylethyl)amino]ethyl}sulfanyl)adenosine	4
ATP	ADENOSINE-5'-TRIPHOSPHATE	4
CAmetal	CALCIUM ION	4
IOD	IODIDE ION	4
UNX	UNKNOWN ATOM OR ION	4
1V2	(2R,4S)-1-[2-(4-{[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]amino}phenyl)ethyl]-2-(hydroxymethyl)piperidin-4-ol	3
5NB	5'-amino-8-bromo-5'-deoxyadenosine	2
ADP	ADENOSINE-5'-DIPHOSPHATE	2
DTA	(2S,3S,4R,5R,2'S,3'S,4'R,5'R)-2,2'-[DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)TETRAHYDROFURAN-3,4-DIOL]	2
GYR	{(2R)-1-[4-({3-METHYL-5-[(PHENYLSULFONYL)METHYL]PHENOXY}METHYL)BENZYL]PYRROLIDIN-2-YL}METHANOL	2
MTA	5'-DEOXY-5'-METHYLTHIOADENOSINE	2