6G5W: KDM4A with compound YP-03-038

Crystal Structure of KDM4A with compound YP-03-038. Determined by X-ray diffraction at 1.83 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,233
Mol. weight: 84.94 kDa
Ligands: ENZ, CIT, NI, ZN
Released: 10 Apr 2019

Explore 6G5W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G5W contains 47 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: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	13-15	3
β-strand	16-17	2	1
α-helix	21-24	4
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	1
α-helix	48-50	3
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	158-164	7
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
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	329-333	5
α-helix	345-347	3
α-helix	348-351	4

Chain B: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	16-17	2	5
α-helix	21-25	5
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	5
α-helix	48-50	3
β-strand	66-67	2	6
β-strand	71-78	8	7
β-strand	81-88	8	7
α-helix	89-91	3
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	156-158	3
α-helix	159-162	4
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	318-324	7
α-helix	326-333	8
α-helix	346-347	2
α-helix	348-350	3

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

>6G5W_1 Lysine-specific demethylase 4A (chains A, B)
MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYD
DIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERK
YWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGM
WKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRH
KMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYG
KQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL

Ligands and cofactors

ID	Name	Formula	Copies
ENZ	(4~{R})-5-methyl-4-phenyl-2-pyridin-2-yl-pyrazolidin-3-one	C15 H15 N3 O	1
CIT	Citric acid	C6 H8 O7	3
NI	Nickel (II) ion	Ni	4
ZN	Zinc ion	Zn	2

Water and common crystallization additives (NA, EDO) are not listed.

Primary citation

Enhanced Properties of a Benzimidazole Benzylpyrazole Lysine Demethylase Inhibitor: Mechanism-of-Action, Binding Site Analysis, and Activity in Cellular Models of Prostate Cancer. Carter, D.M., Specker, E., Malecki, P.H. et al. J Med Chem (2021) 64:14266-14282. DOI 10.1021/acs.jmedchem.1c00693 · 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…
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
5D6W 1.99 Å, Crystal structure of double tudor domain of human lysine demethylase KDM4A

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