Atomistry » Chlorine » PDB 6h4j-6hb2 » 6h4t
Atomistry »
  Chlorine »
    PDB 6h4j-6hb2 »
      6h4t »

Chlorine in PDB 6h4t: Crystal Structure of Human KDM4A in Complex with Compound 19A

Protein crystallography data

The structure of Crystal Structure of Human KDM4A in Complex with Compound 19A, PDB code: 6h4t was solved by Y.V.Le Bihan, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.860, 101.812, 142.680, 90.00, 99.20, 90.00
R / Rfree (%) 17.3 / 21.6

Other elements in 6h4t:

The structure of Crystal Structure of Human KDM4A in Complex with Compound 19A also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human KDM4A in Complex with Compound 19A (pdb code 6h4t). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human KDM4A in Complex with Compound 19A, PDB code: 6h4t:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6h4t

Go back to Chlorine Binding Sites List in 6h4t
Chlorine binding site 1 out of 4 in the Crystal Structure of Human KDM4A in Complex with Compound 19A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human KDM4A in Complex with Compound 19A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:73.6
occ:1.00
O A:HOH655 2.9 51.2 1.0
NH1 A:ARG98 3.1 64.6 1.0
CE2 A:PHE283 3.9 34.5 1.0
CE1 A:PHE202 4.1 34.5 1.0
CZ A:PHE202 4.1 35.7 1.0
CD A:ARG98 4.2 28.1 1.0
CZ A:ARG98 4.2 72.9 1.0
CZ A:PHE283 4.3 32.6 1.0
O A:TYR59 4.5 52.2 1.0
NE A:ARG98 4.6 48.9 1.0
CD1 A:PHE202 4.8 32.6 1.0
CE2 A:PHE202 4.9 38.2 1.0
OD1 A:ASP63 4.9 63.4 1.0
O A:HOH657 4.9 55.5 1.0

Chlorine binding site 2 out of 4 in 6h4t

Go back to Chlorine Binding Sites List in 6h4t
Chlorine binding site 2 out of 4 in the Crystal Structure of Human KDM4A in Complex with Compound 19A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human KDM4A in Complex with Compound 19A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:72.7
occ:1.00
O B:HOH741 3.4 45.5 1.0
O B:TYR59 3.6 46.2 1.0
CE1 B:PHE202 3.9 31.2 1.0
CZ B:PHE202 4.0 29.3 1.0
CD1 B:PHE202 4.1 31.2 1.0
CB B:TYR59 4.3 37.6 1.0
NH1 B:ARG98 4.4 48.9 1.0
CE2 B:PHE202 4.4 31.3 1.0
C B:TYR59 4.5 46.3 1.0
CG B:PHE202 4.6 29.6 1.0
CE2 B:PHE283 4.7 34.9 1.0
O B:HOH588 4.7 46.9 1.0
CD2 B:PHE202 4.7 28.9 1.0

Chlorine binding site 3 out of 4 in 6h4t

Go back to Chlorine Binding Sites List in 6h4t
Chlorine binding site 3 out of 4 in the Crystal Structure of Human KDM4A in Complex with Compound 19A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human KDM4A in Complex with Compound 19A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:71.2
occ:1.00
O C:HOH621 2.8 54.0 1.0
NH1 C:ARG98 3.5 43.4 1.0
O C:TYR59 4.0 56.1 1.0
CE2 C:PHE283 4.1 46.5 1.0
CE1 C:PHE202 4.4 41.9 1.0
CD C:ARG98 4.4 43.2 1.0
CZ C:ARG98 4.4 62.5 1.0
CZ C:PHE202 4.5 40.4 1.0
CZ C:PHE283 4.6 44.0 1.0
OD1 C:ASP63 4.7 59.3 1.0
NE C:ARG98 4.8 55.1 1.0
OD1 C:ASP60 5.0 66.0 1.0

Chlorine binding site 4 out of 4 in 6h4t

Go back to Chlorine Binding Sites List in 6h4t
Chlorine binding site 4 out of 4 in the Crystal Structure of Human KDM4A in Complex with Compound 19A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human KDM4A in Complex with Compound 19A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:90.3
occ:1.00
NH2 D:ARG98 3.5 60.7 1.0
NH1 D:ARG98 3.9 86.4 1.0
O D:HOH687 4.0 43.8 1.0
CD1 D:PHE202 4.1 33.9 1.0
CE1 D:PHE202 4.1 34.7 1.0
CZ D:ARG98 4.2 83.8 1.0
O D:TYR59 4.2 65.2 1.0
CZ D:PHE202 4.4 33.9 1.0
CG D:PHE202 4.4 31.3 1.0
CB D:TYR59 4.4 49.2 1.0
CE2 D:PHE202 4.7 36.2 1.0
CD2 D:PHE202 4.7 33.2 1.0
C D:TYR59 4.9 65.3 1.0

Reference:

Y.V.Le Bihan, R.M.Lanigan, B.Atrash, M.G.Mclaughlin, S.Velupillai, A.G.Malcolm, K.S.England, G.F.Ruda, N.Y.Mok, A.Tumber, K.Tomlin, H.Saville, E.Shehu, C.Mcandrew, L.Carmichael, J.M.Bennett, F.Jeganathan, P.Eve, A.Donovan, A.Hayes, F.Wood, F.I.Raynaud, O.Fedorov, P.E.Brennan, R.Burke, R.L.M.Van Montfort, O.W.Rossanese, J.Blagg, V.Bavetsias. C8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-Ones: Studies Towards the Identification of Potent, Cell Penetrant Jumonji C Domain Containing Histone Lysine Demethylase 4 Subfamily (KDM4) Inhibitors, Compound Profiling in Cell-Based Target Engagement Assays. Eur.J.Med.Chem. V. 177 316 2019.
ISSN: ISSN 0223-5234
PubMed: 31158747
DOI: 10.1016/J.EJMECH.2019.05.041
Page generated: Sun Jul 28 00:35:56 2024

Last articles

Cl in 5SD0
Cl in 5SCZ
Cl in 5SBE
Cl in 5SCP
Cl in 5SBD
Cl in 5SBC
Cl in 5SBA
Cl in 5SBB
Cl in 5SB9
Cl in 5SB8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy