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Chlorine in PDB 9fmr: Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835

Enzymatic activity of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835

All present enzymatic activity of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835:
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835, PDB code: 9fmr was solved by K.Anand, M.Schmitz, M.Geyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.71 / 3.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 249.521, 249.521, 218.535, 90, 90, 120
R / Rfree (%) 20.8 / 25

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 (pdb code 9fmr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835, PDB code: 9fmr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 9fmr

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Chlorine binding site 1 out of 6 in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1101

b:285.6
occ:1.00
 CL1 B:RMF1101 0.0 285.6 1.0
C19 B:RMF1101 1.8 232.4 1.0
C18 B:RMF1101 2.7 229.3 1.0
C20 B:RMF1101 2.8 227.1 1.0
CL2 B:RMF1101 3.2 253.4 1.0
CD A:ARG947 3.6 216.9 1.0
CB A:ARG928 4.0 229.6 1.0
C21 B:RMF1101 4.1 226.8 1.0
C16 B:RMF1101 4.1 238.5 1.0
O B:ILE733 4.1 207.4 1.0
CA A:ARG928 4.3 229.0 1.0
O A:ARG928 4.3 214.2 1.0
CG A:ARG928 4.3 240.3 1.0
NE A:ARG947 4.3 218.9 1.0
CD A:ARG928 4.3 244.4 1.0
NE A:ARG928 4.4 242.0 1.0
NH1 A:ARG947 4.4 221.9 1.0
CD1 A:PHE949 4.5 242.6 1.0
C17 B:RMF1101 4.6 238.1 1.0
CZ A:ARG947 4.6 235.5 1.0
C A:ARG928 4.8 236.1 1.0
CG A:ARG947 4.8 211.5 1.0
CE1 A:PHE949 4.9 248.6 1.0
C B:ILE733 5.0 211.1 1.0

Chlorine binding site 2 out of 6 in 9fmr

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Chlorine binding site 2 out of 6 in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1101

b:253.4
occ:1.00
 CL2 B:RMF1101 0.0 253.4 1.0
C20 B:RMF1101 1.8 227.1 1.0
C21 B:RMF1101 2.7 226.8 1.0
C19 B:RMF1101 2.8 232.4 1.0
NE A:ARG947 3.0 218.9 1.0
CZ A:ARG947 3.2 235.5 1.0
CL1 B:RMF1101 3.2 285.6 1.0
NH2 A:ARG947 3.5 230.3 1.0
ND2 A:ASN907 3.5 218.2 1.0
CD A:ARG947 3.6 216.9 1.0
NH1 A:ARG947 3.8 221.9 1.0
OD1 A:ASN907 3.8 202.3 1.0
CG A:ASN907 4.0 213.4 1.0
C18 B:RMF1101 4.1 229.3 1.0
C17 B:RMF1101 4.1 238.1 1.0
NH1 A:ARG928 4.1 232.6 1.0
O B:ILE732 4.1 226.0 1.0
CZ A:ARG928 4.2 233.9 1.0
NE A:ARG928 4.2 242.0 1.0
CD A:ARG928 4.3 244.4 1.0
CA B:ILE733 4.4 207.2 1.0
CG2 B:ILE733 4.4 207.2 1.0
C16 B:RMF1101 4.6 238.5 1.0
CB B:ILE733 4.6 212.2 1.0
O A:ASN907 4.6 231.0 1.0
NH2 A:ARG928 4.8 220.4 1.0
C B:ILE732 5.0 207.2 1.0

Chlorine binding site 3 out of 6 in 9fmr

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Chlorine binding site 3 out of 6 in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1101

b:245.9
occ:1.00
 CL1 E:RMF1101 0.0 245.9 1.0
C19 E:RMF1101 1.8 232.3 1.0
C18 E:RMF1101 2.8 234.4 1.0
C20 E:RMF1101 2.8 235.2 1.0
CL2 E:RMF1101 3.2 244.7 1.0
CD D:ARG947 3.7 243.9 1.0
NE D:ARG928 3.9 229.2 1.0
O E:ILE733 4.0 254.7 1.0
CD D:ARG928 4.0 229.7 1.0
C21 E:RMF1101 4.1 223.3 1.0
C16 E:RMF1101 4.1 221.5 1.0
CB D:ARG928 4.1 222.7 1.0
CG D:ARG928 4.2 218.1 1.0
NE D:ARG947 4.4 210.1 1.0
CA D:ARG928 4.5 216.6 1.0
C17 E:RMF1101 4.6 208.0 1.0
O D:ARG928 4.7 182.8 1.0
CD1 D:PHE949 4.8 265.9 1.0
CG D:ARG947 4.9 247.1 1.0
C E:ILE733 4.9 248.2 1.0
CZ D:ARG947 5.0 223.6 1.0

Chlorine binding site 4 out of 6 in 9fmr

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Chlorine binding site 4 out of 6 in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1101

b:244.7
occ:1.00
 CL2 E:RMF1101 0.0 244.7 1.0
C20 E:RMF1101 1.8 235.2 1.0
C21 E:RMF1101 2.7 223.3 1.0
C19 E:RMF1101 2.8 232.3 1.0
CZ D:ARG947 3.2 223.6 1.0
CL1 E:RMF1101 3.2 245.9 1.0
NH1 D:ARG947 3.2 240.5 1.0
NE D:ARG947 3.4 210.1 1.0
ND2 D:ASN907 3.5 205.8 1.0
NE D:ARG928 3.5 229.2 1.0
NH2 D:ARG947 3.7 216.8 1.0
CD D:ARG928 3.7 229.7 1.0
CD D:ARG947 3.8 243.9 1.0
OD1 D:ASN907 3.9 203.9 1.0
CG D:ASN907 4.0 199.3 1.0
C18 E:RMF1101 4.1 234.4 1.0
C17 E:RMF1101 4.1 208.0 1.0
CZ D:ARG928 4.2 215.4 1.0
CG2 E:ILE733 4.3 202.6 1.0
O E:ILE732 4.4 250.1 1.0
CA E:ILE733 4.4 224.6 1.0
CB E:ILE733 4.5 214.8 1.0
C16 E:RMF1101 4.6 221.5 1.0
NH2 D:ARG928 4.6 191.7 1.0
O D:ASN907 4.7 213.6 1.0
NH1 D:ARG928 4.9 223.1 1.0
CG D:ARG928 4.9 218.1 1.0
O E:ILE733 5.0 254.7 1.0

Chlorine binding site 5 out of 6 in 9fmr

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Chlorine binding site 5 out of 6 in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1101

b:335.3
occ:1.00
 CL1 H:RMF1101 0.0 335.3 1.0
C19 H:RMF1101 1.8 264.9 1.0
NH1 G:ARG947 2.5 265.2 1.0
C18 H:RMF1101 2.7 247.8 1.0
C20 H:RMF1101 2.8 264.4 1.0
CL2 H:RMF1101 3.2 316.1 1.0
CZ G:ARG947 3.3 269.2 1.0
CD G:ARG947 3.6 266.5 1.0
NE G:ARG947 3.7 274.1 1.0
C21 H:RMF1101 4.1 257.5 1.0
C16 H:RMF1101 4.1 247.8 1.0
O H:ILE733 4.1 237.3 1.0
CB G:ARG947 4.3 224.4 1.0
NH2 G:ARG947 4.3 253.2 1.0
O H:ILE732 4.3 244.9 1.0
CG G:ARG928 4.3 287.9 1.0
CD1 G:PHE949 4.5 263.0 1.0
CA H:ILE733 4.5 236.0 1.0
CG G:ARG947 4.5 235.9 1.0
C17 H:RMF1101 4.6 245.5 1.0
C H:ILE733 4.6 234.3 1.0
CE1 G:PHE949 4.7 268.6 1.0
CB G:ARG928 4.7 263.5 1.0
O G:ASP948 4.8 261.9 1.0

Chlorine binding site 6 out of 6 in 9fmr

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Chlorine binding site 6 out of 6 in the Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1101

b:316.1
occ:1.00
 CL2 H:RMF1101 0.0 316.1 1.0
C20 H:RMF1101 1.8 264.4 1.0
ND2 G:ASN907 2.7 253.0 1.0
C21 H:RMF1101 2.7 257.5 1.0
C19 H:RMF1101 2.8 264.9 1.0
NE G:ARG947 3.1 274.1 1.0
CZ G:ARG947 3.1 269.2 1.0
CG G:ASN907 3.2 247.4 1.0
CL1 H:RMF1101 3.2 335.3 1.0
OD1 G:ASN907 3.2 254.4 1.0
NH2 G:ARG947 3.5 253.2 1.0
CD G:ARG947 3.6 266.5 1.0
NH1 G:ARG947 3.6 265.2 1.0
O G:ASN907 4.0 234.6 1.0
O H:ILE732 4.0 244.9 1.0
C18 H:RMF1101 4.1 247.8 1.0
C17 H:RMF1101 4.1 245.5 1.0
CB G:ASN907 4.3 247.3 1.0
CG2 H:ILE733 4.5 210.0 1.0
C16 H:RMF1101 4.6 247.8 1.0
C G:ASN907 4.7 238.3 1.0
CA H:ILE733 4.7 236.0 1.0
C H:ILE732 4.9 242.9 1.0
CB H:ILE733 5.0 223.0 1.0

Reference:

K.Anand, M.Schmitz, M.Geyer. Structure of DDB1/CDK12/Cyclin K with Molecular Glue Sr-4835 To Be Published.
Page generated: Thu Oct 31 18:12:26 2024

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