Atomistry » Nickel » PDB 5tvr-5xgz » 5vgi
Atomistry »
  Nickel »
    PDB 5tvr-5xgz »
      5vgi »

Nickel in PDB 5vgi: Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352

Protein crystallography data

The structure of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352, PDB code: 5vgi was solved by D.J.Hosfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.318, 101.594, 141.893, 90.00, 99.64, 90.00
R / Rfree (%) 18.9 / 24.9

Other elements in 5vgi:

The structure of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 (pdb code 5vgi). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352, PDB code: 5vgi:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 5vgi

Go back to Nickel Binding Sites List in 5vgi
Nickel binding site 1 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:28.8
occ:1.00
N4 A:9DJ503 2.1 31.5 1.0
OE2 A:GLU190 2.1 29.3 1.0
O A:HOH609 2.2 25.3 1.0
NE2 A:HIS188 2.2 29.4 1.0
O A:HOH620 2.3 26.8 1.0
NE2 A:HIS276 2.3 23.1 1.0
C3 A:9DJ503 2.9 34.4 1.0
C5 A:9DJ503 3.0 30.2 1.0
CE1 A:HIS188 3.1 29.3 1.0
CD A:GLU190 3.1 29.9 1.0
CE1 A:HIS276 3.1 22.3 1.0
CD2 A:HIS188 3.3 27.4 1.0
CD2 A:HIS276 3.4 20.1 1.0
OE1 A:GLU190 3.5 29.5 1.0
ND1 A:HIS188 4.3 27.6 1.0
C2 A:9DJ503 4.3 34.1 1.0
ND1 A:HIS276 4.3 23.1 1.0
C6 A:9DJ503 4.3 32.8 1.0
CG A:HIS188 4.4 25.9 1.0
CG A:HIS276 4.5 21.0 1.0
CG A:GLU190 4.5 25.8 1.0
OG A:SER196 4.5 26.0 1.0
C1 A:9DJ503 4.9 35.3 1.0

Nickel binding site 2 out of 4 in 5vgi

Go back to Nickel Binding Sites List in 5vgi
Nickel binding site 2 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:35.4
occ:1.00
O B:HOH642 2.1 37.2 1.0
N4 B:9DJ503 2.2 32.7 1.0
NE2 B:HIS276 2.2 26.1 1.0
OE2 B:GLU190 2.2 34.1 1.0
NE2 B:HIS188 2.2 29.2 1.0
O B:HOH606 2.4 27.7 1.0
C5 B:9DJ503 3.0 33.4 1.0
C3 B:9DJ503 3.1 35.9 1.0
CE1 B:HIS188 3.1 28.8 1.0
CD2 B:HIS276 3.1 23.7 1.0
CD B:GLU190 3.1 30.4 1.0
CE1 B:HIS276 3.2 26.0 1.0
CD2 B:HIS188 3.2 31.0 1.0
OE1 B:GLU190 3.4 28.6 1.0
ND1 B:HIS188 4.2 28.0 1.0
CG B:HIS276 4.3 23.9 1.0
ND1 B:HIS276 4.3 25.9 1.0
C6 B:9DJ503 4.3 34.2 1.0
CG B:HIS188 4.3 28.8 1.0
C2 B:9DJ503 4.4 34.3 1.0
CG B:GLU190 4.5 28.6 1.0
OG B:SER196 4.6 27.0 1.0
NZ B:LYS241 4.7 48.0 1.0
C1 B:9DJ503 4.9 33.4 1.0

Nickel binding site 3 out of 4 in 5vgi

Go back to Nickel Binding Sites List in 5vgi
Nickel binding site 3 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni501

b:26.7
occ:1.00
NE2 C:HIS276 2.1 21.0 1.0
O C:HOH619 2.2 24.6 1.0
N4 C:9DJ503 2.2 29.5 1.0
O C:HOH617 2.2 28.4 1.0
OE2 C:GLU190 2.2 25.9 1.0
NE2 C:HIS188 2.2 28.6 1.0
CE1 C:HIS188 3.0 26.4 1.0
C3 C:9DJ503 3.0 30.1 1.0
CE1 C:HIS276 3.1 19.5 1.0
C5 C:9DJ503 3.1 31.4 1.0
CD C:GLU190 3.2 25.4 1.0
CD2 C:HIS276 3.2 18.1 1.0
CD2 C:HIS188 3.3 27.2 1.0
OE1 C:GLU190 3.5 23.6 1.0
ND1 C:HIS188 4.2 25.8 1.0
ND1 C:HIS276 4.2 18.1 1.0
CG C:HIS276 4.3 18.8 1.0
C2 C:9DJ503 4.4 32.2 1.0
CG C:HIS188 4.4 24.6 1.0
C6 C:9DJ503 4.4 28.9 1.0
OG C:SER196 4.4 23.9 1.0
CG C:GLU190 4.5 23.4 1.0
C1 C:9DJ503 4.9 30.9 1.0

Nickel binding site 4 out of 4 in 5vgi

Go back to Nickel Binding Sites List in 5vgi
Nickel binding site 4 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni501

b:30.6
occ:1.00
N4 D:9DJ503 2.1 32.3 1.0
O D:HOH614 2.1 28.9 1.0
OE2 D:GLU190 2.2 27.0 1.0
O D:HOH634 2.2 22.0 1.0
NE2 D:HIS188 2.2 29.2 1.0
NE2 D:HIS276 2.3 23.9 1.0
C3 D:9DJ503 3.0 33.2 1.0
C5 D:9DJ503 3.0 29.2 1.0
CE1 D:HIS188 3.1 28.1 1.0
CD D:GLU190 3.1 26.6 1.0
CE1 D:HIS276 3.2 24.0 1.0
CD2 D:HIS188 3.2 28.7 1.0
CD2 D:HIS276 3.3 22.1 1.0
OE1 D:GLU190 3.4 26.5 1.0
ND1 D:HIS188 4.2 28.9 1.0
C2 D:9DJ503 4.3 35.8 1.0
CG D:HIS188 4.3 26.5 1.0
C6 D:9DJ503 4.4 31.0 1.0
ND1 D:HIS276 4.4 24.1 1.0
CG D:HIS276 4.4 23.9 1.0
CG D:GLU190 4.6 24.1 1.0
OG D:SER196 4.6 26.3 1.0
C1 D:9DJ503 4.9 33.0 1.0

Reference:

Y.K.Chen, T.Bonaldi, A.Cuomo, J.R.Del Rosario, D.J.Hosfield, T.Kanouni, S.C.Kao, C.Lai, N.A.Lobo, J.Matuszkiewicz, A.Mcgeehan, S.M.O'connell, L.Shi, J.A.Stafford, R.K.Stansfield, J.M.Veal, M.S.Weiss, N.Y.Yuen, M.B.Wallace. Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. Acs Med Chem Lett V. 8 869 2017.
ISSN: ISSN 1948-5875
PubMed: 28835804
DOI: 10.1021/ACSMEDCHEMLETT.7B00220
Page generated: Thu Oct 10 08:07:35 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy