6Q9W: Compound 15

X-ray structure of compound 15 bound to HdmX: Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes. Determined by X-ray diffraction at 1.55 Å resolution. Released 15 May 2019.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,682
Mol. weight: 24.73 kDa
Ligands: HRT, O4B
Released: 15 May 2019

Explore 6Q9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q9W contains 8 α-helices and 14 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	1
α-helix	32-40	9
β-strand	48	1	1
α-helix	50-63	14
β-strand	67	1	2
β-strand	74-76	3	2
α-helix	81-86	6
β-strand	90-92	3	2
α-helix	97-106	10
β-strand	107-110	4	1

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	3
β-strand	29-30	2	4
α-helix	32-40	9
β-strand	48	1	3
α-helix	50-63	14
β-strand	67	1	5
β-strand	74-76	3	5
α-helix	81-86	6
β-strand	90-92	3	5
β-strand	95	1	5
α-helix	97-106	10
β-strand	107-108	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein Mdm4	A, B	protein	100	Homo sapiens	O15151 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6Q9W_1 Protein Mdm4 (chains A, B)
GPDSASRISPGQINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQ
HMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT

Ligands and cofactors

ID	Name	Formula	Copies
HRT	(4~{S})-4-(4-chlorophenyl)-5-[(1~{S})-1-(3-chlorophenyl)ethyl]-2-(2,4-dimethoxy…	C28 H27 Cl2 N5 O3	2
O4B	1,4,7,10,13,16-hexaoxacyclooctadecane	C12 H24 O6	4

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

Primary citation

Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes. Kallen, J., Izaac, A., Chau, S. et al. ChemMedChem (2019) 14:1305-1314. DOI 10.1002/cmdc.201900201 · PubMed

Other PDB entries of the same protein (UniProt O15151 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q9Y 1.2 Å, HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structural states of Hdm2 and…
3FEA 1.33 Å, Crystal Structure of HdmX bound to the p53-peptidomimetic…
3FE7 1.35 Å, Crystal Structure of HdmX bound to the p53-peptidomimetic…
3FDO 1.4 Å, Structure of human MDMX in complex with high affinity peptide
3LBJ 1.5 Å, Structure of human MDMX protein in complex with a small molecule inhibitor
4RXZ 1.55 Å, Crystal Structure of MDMX phosporylated Tyr99 in complex with a 12-mer peptide
3EQY 1.63 Å, Crystal structure of human MDMX in complex with a 12-mer peptide inhibitor
7C3Y 1.63 Å, Crystal structure of the N-terminal domain of human MdmX protein in complex with Nutlin3a
7C44 1.65 Å, Crystal structure of the p53-binding domain of human MdmX protein in complex with Nutlin3a
8HDG 1.73 Å, Small peptide enhances the binding of nutline-3a to MdmX
3JZP 1.74 Å, Human MDMX liganded with a 12mer peptide inhibitor (pDI6W)
3JZO 1.8 Å, Human MDMX liganded with a 12mer peptide (pDI)

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