Zinc in PDB 5vkc: Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor

The structure of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor, PDB code: 5vkc was solved by R.A.Judge, A.J.Souers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.81 / 2.31
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	63.920, 63.920, 91.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor (pdb code 5vkc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor, PDB code: 5vkc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:48.5 occ:1.00 NE2 A:HIS224 2.1 46.6 1.0 CD2 A:HIS224 3.1 46.9 1.0 CE1 A:HIS224 3.1 46.2 1.0 N51 A:9EA401 3.9 51.8 1.0 CB A:ASN223 4.1 44.7 1.0 C27 A:9EA401 4.1 51.8 1.0 CG A:HIS224 4.2 45.3 1.0 ND1 A:HIS224 4.2 47.2 1.0 C36 A:9EA401 4.4 53.8 1.0 C13 A:9EA401 4.4 51.3 1.0 OD1 A:ASN223 4.5 67.8 1.0 C38 A:9EA401 4.6 55.0 1.0 C12 A:9EA401 4.7 53.7 1.0 CG A:ASN223 4.8 68.7 1.0 C35 A:9EA401 5.0 51.3 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:54.1 occ:1.00 N47 A:9EA401 2.2 37.2 1.0 C18 A:9EA401 3.1 35.9 1.0 C17 A:9EA401 3.1 36.8 1.0 C24 A:9EA401 4.4 35.6 1.0 C5 A:9EA401 4.4 37.1 1.0 C41 A:9EA401 4.5 40.7 1.0 C11 A:9EA401 4.9 35.4 1.0 N50 A:9EA401 4.9 40.4 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:49.6 occ:1.00 O A:HOH537 2.1 42.5 1.0 OD2 A:ASP256 2.1 55.4 1.0 NE2 A:HIS252 2.1 35.6 1.0 CG A:ASP256 2.9 47.9 1.0 CD2 A:HIS252 3.0 36.0 1.0 OD1 A:ASP256 3.1 48.8 1.0 CE1 A:HIS252 3.2 35.3 1.0 CG A:HIS252 4.2 34.1 1.0 CB A:ASP256 4.3 37.5 1.0 ND1 A:HIS252 4.3 35.9 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:37.0 occ:1.00 ND1 A:HIS252 1.9 35.9 1.0 O A:HOH515 2.2 40.4 1.0 CG A:HIS252 2.9 34.1 1.0 CE1 A:HIS252 2.9 35.3 1.0 CB A:HIS252 3.3 30.1 1.0 NH1 A:ARG248 3.6 57.1 1.0 NE2 A:HIS252 4.0 35.6 1.0 CD2 A:HIS252 4.0 36.0 1.0 CA A:HIS252 4.6 29.7 1.0 CZ A:ARG248 4.7 72.9 1.0 O A:ARG248 5.0 39.4 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:97.3 occ:1.00 OD1 A:ASP242 2.2 64.1 1.0 CG A:ASP242 3.2 62.9 1.0 OD2 A:ASP242 3.5 67.3 1.0 ND2 A:ASN239 4.5 75.3 1.0 CB A:ASP242 4.5 52.0 1.0 OD1 A:ASN239 4.6 81.5 1.0 O A:ASP236 4.6 66.0 1.0 CG A:ASN239 5.0 84.9 1.0 CA A:ASP242 5.0 49.9 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:93.3 occ:1.00 OD2 A:ASP241 2.5 90.7 1.0 CG A:ASP241 3.3 79.8 1.0 OD1 A:ASP241 3.3 80.4 1.0 CB A:ASP241 4.7 62.1 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:51.3 occ:1.00 O B:HOH541 1.9 43.5 1.0 NE2 A:HIS320 2.1 46.6 1.0 N47 B:9EA401 2.2 37.2 1.0 O A:HOH540 2.3 45.5 1.0 CE1 A:HIS320 2.9 46.5 1.0 C17 B:9EA401 3.1 36.9 1.0 C18 B:9EA401 3.1 34.4 1.0 CD2 A:HIS320 3.2 46.5 1.0 ND1 A:HIS320 4.1 47.0 1.0 CG A:HIS320 4.2 44.8 1.0 C5 B:9EA401 4.4 36.3 1.0 C24 B:9EA401 4.4 34.1 1.0 C41 B:9EA401 4.5 40.1 1.0 N50 B:9EA401 4.9 39.8 1.0 C11 B:9EA401 5.0 33.4 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:49.4 occ:1.00 O B:HOH518 2.1 45.8 1.0 NE2 B:HIS224 2.1 46.0 1.0 CD2 B:HIS224 3.1 46.4 1.0 CE1 B:HIS224 3.2 45.6 1.0 N51 B:9EA401 3.9 50.7 1.0 C36 B:9EA401 4.0 52.2 1.0 CB B:ASN223 4.1 43.5 1.0 C27 B:9EA401 4.2 52.0 1.0 CG B:HIS224 4.2 45.2 1.0 C38 B:9EA401 4.2 52.6 1.0 ND1 B:HIS224 4.3 46.8 1.0 OD1 B:ASN223 4.4 71.8 1.0 C13 B:9EA401 4.5 51.4 1.0 C12 B:9EA401 4.7 54.4 1.0 CG B:ASN223 4.8 70.1 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:36.0 occ:1.00 ND1 B:HIS252 1.9 34.7 1.0 O B:HOH532 2.3 40.0 1.0 CE1 B:HIS252 2.9 34.0 1.0 CG B:HIS252 2.9 32.8 1.0 CB B:HIS252 3.3 29.1 1.0 NH1 B:ARG248 3.6 67.4 1.0 NE2 B:HIS252 4.0 34.3 1.0 CD2 B:HIS252 4.0 34.7 1.0 CA B:HIS252 4.6 29.0 1.0 CZ B:ARG248 4.7 81.3 1.0 O B:ARG248 5.0 40.2 1.0 NH2 B:ARG248 5.0 63.8 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Mcl-1 in Complex with A Bim Competitive Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:48.8 occ:1.00 O B:HOH533 1.9 37.4 1.0 OD2 B:ASP256 2.0 51.4 1.0 NE2 B:HIS252 2.1 34.3 1.0 CG B:ASP256 2.8 44.2 1.0 CD2 B:HIS252 2.9 34.7 1.0 OD1 B:ASP256 3.0 46.5 1.0 CE1 B:HIS252 3.2 34.0 1.0 O A:GLU322 3.7 69.2 1.0 CG B:HIS252 4.1 32.8 1.0 CB B:ASP256 4.2 34.1 1.0 ND1 B:HIS252 4.3 34.7 1.0 C A:GLU322 4.6 0.5 1.0 O B:HIS252 5.0 34.2 1.0

M.Bruncko, L.Wang, G.S.Sheppard, D.C.Phillips, S.K.Tahir, J.Xue, S.Erickson, S.Fidanze, E.Fry, L.Hasvold, G.J.Jenkins, S.Jin, R.A.Judge, P.J.Kovar, D.Madar, P.Nimmer, C.Park, A.M.Petros, S.H.Rosenberg, M.L.Smith, X.Song, C.Sun, Z.F.Tao, X.Wang, Y.Xiao, H.Zhang, C.Tse, J.D.Leverson, S.W.Elmore, A.J.Souers. Structure-Guided Design of A Series of Mcl-1 Inhibitors with High Affinity and Selectivity. J. Med. Chem. V. 58 2180 2015.
ISSN: ISSN 1520-4804
PubMed: 25679114
DOI: 10.1021/JM501258M