5ANQ: Lysine-specific demethylase 4A

inhibitors of JumonjiC domain-containing histone demethylases. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Mar 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 6,125
Mol. weight: 84.92 kDa
Ligands: 5YQ, FE2, ZN
Released: 23 Mar 2016

Explore 5ANQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ANQ contains 48 α-helices and 34 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	15-17	3	1
α-helix	21-24	4
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	1
β-strand	66-67	2	2
β-strand	71-78	8	3
β-strand	81-88	8	3
β-strand	92-93	2	2
α-helix	94-102	9
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	3
β-strand	133-137	5	1
α-helix	156-158	3
α-helix	159-164	6
β-strand	175-179	5	1
β-strand	184-188	5	4
α-helix	189-190	2
α-helix	191-193	3
β-strand	195-203	9	1
β-strand	206-211	6	4
α-helix	213-215	3
α-helix	216-226	11
α-helix	228-233	6
α-helix	237-240	4
β-strand	243-245	3	3
α-helix	247-252	6
β-strand	258-262	5	4
α-helix	263	1
β-strand	267-270	4	1
β-strand	275-280	6	4
β-strand	284-291	8	1
α-helix	296-302	7
α-helix	303-306	4
α-helix	318-324	7
α-helix	326-328	3
α-helix	329-333	5
α-helix	339-341	3
α-helix	346-347	2
α-helix	348-350	3

Chain B: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15-17	3	5
α-helix	21-25	5
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	5
β-strand	66-67	2	6
β-strand	71-78	8	7
β-strand	81-88	8	7
β-strand	92-93	2	6
α-helix	94-102	9
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	7
β-strand	133-137	5	5
α-helix	156-160	5
β-strand	175-179	5	5
β-strand	184-188	5	8
α-helix	189-190	2
α-helix	191-193	3
β-strand	195-203	9	5
β-strand	206-211	6	8
α-helix	213-215	3
α-helix	216-226	11
α-helix	228-233	6
α-helix	237-240	4
β-strand	243-245	3	7
α-helix	247-252	6
β-strand	258-262	5	8
α-helix	263	1
β-strand	267-270	4	5
β-strand	275-280	6	8
β-strand	284-291	8	5
α-helix	296-302	7
α-helix	303-306	4
α-helix	318-324	7
α-helix	326-333	8
α-helix	339-341	3
α-helix	346-347	2
α-helix	348-352	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A, B	protein	359	HOMO SAPIENS	O75164 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5ANQ_1 LYSINE-SPECIFIC DEMETHYLASE 4A (chains A, B)
MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYD
DIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERK
YWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGM
WKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRH
KMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYG
KQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL

Ligands and cofactors

ID	Name	Formula	Copies
5YQ	2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid	C16 H13 N5 O2	2
FE2	FE (II) ion	Fe	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

Substituted 2-(2-Aminopyrimidin-4-Yl)Pyridine-4-Carboxylates as Potent Inhibitors of Jumonjic Domain-Containing Histone Demethylases. Roatsch, M., Robaa, D., Pippel, M. et al. Future Med Chem (2016) 8:1553. DOI 10.4155/FMC.15.188 · PubMed

Other PDB entries of the same protein (UniProt O75164 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GP4 1.59 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D
9GII 1.7 Å, Jumonji domain-containing protein 2A with crystallization epitope mutation R913A
6G5X 1.78 Å, Crystal Structure of KDM4A with compound YP-02-145
2QQR 1.8 Å, JMJD2A hybrid tudor domains
4V2W 1.81 Å, JMJD2A complexed with ni(ii), nog and histone H3K27me3 peptide (16-35)
5VAR 1.83 Å, Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine…
6G5W 1.83 Å, Crystal Structure of KDM4A with compound YP-03-038
9GLE 1.88 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S
2OX0 1.95 Å, Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9
6H8P 1.98 Å, JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
3PDQ 1.99 Å, Crystal structure of JMJD2A complexed with bipyridyl inhibitor
2P5B 1.99 Å, The complex structure of JMJD2A and trimethylated H3K36 peptide

Browse structure collections

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