6UDV: X-ray co-crystal structure of compound 3

X-ray co-crystal structure of compound 3 bound to human Mcl-1. Determined by X-ray diffraction at 1.35 Å resolution. Released 4 Dec 2019.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,439
Mol. weight: 18.52 kDa
Ligands: Q51
Released: 4 Dec 2019

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

Secondary structure: helices and β-sheets

6UDV contains 12 α-helices and 0 β-strands across 1 chain. 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	173-191	19
α-helix	198-199	2
α-helix	203-223	21
α-helix	225-235	11
α-helix	240-244	5
α-helix	246-250	5
α-helix	251-255	5
α-helix	261-280	20
α-helix	284-286	3
α-helix	287-308	22
α-helix	311-319	9
α-helix	322-325	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Induced myeloid leukemia cell differentiation protein Mcl-1	A	protein	157	Homo sapiens	Q07820 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6UDV_1 Induced myeloid leukemia cell differentiation protein Mcl-1 (chains A)
EDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQG
MLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPL
AESITDVLVRTKRDWLVKQRGWDGFVEFFHVEDLEGG

Ligands and cofactors

ID	Name	Formula	Copies
Q51	(4S,7aR,9aR,10S,11E,14S,15R)-6'-chloro-10-hydroxy-14,15-dimethyl-3',4',7a,8,9,9…	C32 H39 Cl N2 O5 S	1

Primary citation

Discovery and in Vivo Evaluation of Macrocyclic Mcl-1 Inhibitors Featuring an alpha-Hydroxy Phenylacetic Acid Pharmacophore or Bioisostere. Rescourio, G., Gonzalez, A.Z., Jabri, S. et al. J Med Chem (2019) 62:10258-10271. DOI 10.1021/acs.jmedchem.9b01310 · PubMed

Other PDB entries of the same protein (UniProt Q07820 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VJP 1.13 Å, Histidine-covalent stapled alpha-helical peptide (155H1) targeting hMcl-1
9PQ7 1.24 Å, MBP-Mcl1 in complex with ligand 21b
9PQ5 1.28 Å, MBP-Mcl1 in complex with ligand 8
9UGP 1.39 Å, Crystal structure of MCL-1 in complex with HRK BH3
8G3S 1.4 Å, MBP-Mcl1 in complex with ligand 11
5W89 1.42 Å, Crystal structure of human Mcl-1 in complex with modified Bim BH3 peptide SAH-MS1-18
5C3F 1.43 Å, Crystal structure of Mcl-1 bound to BID-MM
8G3X 1.46 Å, MBP-Mcl1 in complex with ligand 32
8H7B 1.46 Å, The crystal structure of human mcl1 kinase domain in complex with MCL1-M-EBA
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
6OQD 1.48 Å, Crystal structure of Mcl1 with inhibitor 8
5FC4 1.5 Å, Mcl-1 complexed with small molecule inhibitor

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