X-group (possible homology)

2492 Cytidine deaminase-like

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Ligands and drugs

4,579

Member domains

903

with ligand contacts (≤ 4 Å)

19.7% of members

729

with DrugDomain annotations

15.9% of members

284

with a DrugBank compound

6.2% 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)

7.2

Superclasses per 20 proteins

narrower than 57% 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
Homogeneous metal compounds	84	43.1	1.95×	q < 0.0001
Organic oxygen compounds	14	17.5	0.80×	q = 0.50
Nucleosides, nucleotides, and analogues	17	24.3	0.70×	q = 0.14
Homogeneous non-metal compounds	13	18.9	0.69×	q = 0.21
Benzenoids	4	6.4	0.62×	q = 0.49
Organoheterocyclic compounds	6	13.5	0.44×	q = 0.04
Organic acids and derivatives	5	13.6	0.37×	q = 0.01
Lipids and lipid-like molecules	1	9.8	0.10×	q = 2.3e-3
Miscellaneous inorganic compounds	1	0.1	15×	not tested
Organosulfur compounds	2	1.8	1.11×	not tested
Organic nitrogen compounds	1	2.8	0.36×	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
DB14981	IHP	Phytic acid	25
DB01700	AMZ	AICA ribonucleotide	23
DB02745	URI	Uridine	19
DB03798	DCM	2'-Deoxycytidine-5'-Monophosphate	17
DB03800	DU	Deoxyuridine monophosphate	12
DB03562	THU	Tetrahydrodeoxyuridine	10
DB02452	TTP	Thymidine 5'-triphosphate	9
DB01667	AZG	8-azaguanine	8
DB01643	TMP	Thymidine monophosphate	7
DB02097	CTN	Cytidine	7
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	5
DB03442	326	Acid yellow 54 free acid	5
DB04057	MS1	N-[4-([(2-Amino-4-oxo-1,4-dihydropyrido[3,2-d]pyrimidin-6-yl)methyl]{(2E)-3-[4-carbamoyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazol-5-yl]-2-propenoyl}amino)benzoyl]-L-glutamic acid	5
DB03570	144	Tris-Hydroxymethyl-Methyl-Ammonium	4
DB03939	HPY	(4S)-4-hydroxy-3,4-dihydro-2(1H)-pyrimidinone	4
DB04280	DDN	3,4-Dihydro-2'-deoxyuridine-5'-monophosphate	4
DB02210	HEZ	Hexane-1,6-Diol	3
DB00640	ADN	Adenosine	2
DB01849	DUC	Dihydrouracil	2
DB01972	5GP	Guanosine-5'-Monophosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	766
CL	CHLORIDE ION	50
IHP	INOSITOL HEXAKISPHOSPHATE	42
Kmetal	POTASSIUM ION	35
AMZ	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE	34
MGmetal	MAGNESIUM ION	27
URI	URIDINE	19
DCM	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE	16
CAmetal	CALCIUM ION	14
DU	2'-DEOXYURIDINE-5'-MONOPHOSPHATE	12
THU	TETRAHYDRODEOXYURIDINE	10
TTP	THYMIDINE-5'-TRIPHOSPHATE	9
4UO	2,3-dihydroxanthosine	8
8UM	5-[(5S)-5-ethyl-5-methyl-6-oxo-1,4,5,6-tetrahydropyridin-3-yl]-N-(6-fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)thiophene-2-sulfonamide	8
8US	N-(6-fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)-5-[(3R)-3-hydroxypyrrolidin-1-yl]thiophene-2-sulfonamide	8
AZG	5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL	8
WHC	1~{H}-1,3,5-triazine-2,4-dione	8
CTN	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE	7
TMP	THYMIDINE-5'-PHOSPHATE	7
BW2	N-(4-{[(2-AMINO-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)AMINO]SULFONYL}BENZOYL)GLUTAMIC ACID	6