X-group (possible homology)

286 Diaminopimelate epimerase-like

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Ligands and drugs

1,492

Member domains

230

with ligand contacts (≤ 4 Å)

15.4% of members

192

with DrugDomain annotations

12.9% of members

130

with a DrugBank compound

8.7% 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.

Proteins with classified ligands

Superclasses bound (of 23)

5.8

Superclasses per 20 proteins

narrower than 76% 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 non-metal compounds	8	5.1	1.57×	q = 0.28
Homogeneous metal compounds	6	11.6	0.52×	q = 0.04
Nucleosides, nucleotides, and analogues	0	6.5	0	q = 2.0e-3
Organic acids and derivatives	12	3.7	3.28×	not tested
Organoheterocyclic compounds	6	3.6	1.65×	not tested
Organic oxygen compounds	6	4.7	1.27×	not tested
Benzenoids	1	1.7	0.58×	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
DB02543	PYC	Pyrrole-2-Carboxylate	30
DB02124	HHA	(2s,3s)-Trans-2,3-Dihydro-3-Hydroxyanthranilic Acid	8
DB02239	SHF	Laevulinic Acid	8
DB08847	HYP	Hydroxyproline	6
DB00172	PRO	Proline	4
DB03644	3HA	3-hydroxyanthranilic acid	4
DB04562	TRC	Tricarballylic acid	4
DB09459	TLA	L-tartaric acid	4
DB00139	SIN	Succinic acid	2
DB03590	API	2,6-Diaminopimelic Acid	2
DB04447	DTT	1,4-Dithiothreitol	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
PYC	PYRROLE-2-CARBOXYLATE	30
CL	CHLORIDE ION	24
ZDR	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID	16
ZDP	(2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID	14
HHA	(2S,3S)-TRANS-2,3-DIHYDRO-3-HYDROXYANTHRANILIC ACID	8
IOD	IODIDE ION	8
NQM	(1E)-4-oxobut-1-ene-1,2,4-tricarboxylic acid	8
SHF	LAEVULINIC ACID	8
NAmetal	SODIUM ION	7
CAmetal	CALCIUM ION	6
HYP	4-HYDROXYPROLINE	6
3HA	3-HYDROXYANTHRANILIC ACID	4
7N0	2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid	4
HY3	3-HYDROXYPROLINE	4
TRC	TRICARBALLYLIC ACID	4
TLA	L(+)-TARTARIC ACID	3
A1IAU	2-azanyl-5-(3-hydroxyphenyl)-3-oxidanyl-benzoic acid	2
A1IAV	2-azanyl-5-(4-fluorophenyl)benzoic acid	2
A1IAW	2-azanyl-3-ethoxy-benzoic acid	2
A1IAX	2-azanyl-3-nitro-benzoic acid	2