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Iodine in PDB 7z76: Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb

Protein crystallography data

The structure of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb, PDB code: 7z76 was solved by G.Bader, J.Boettcher, B.Wolkerstorfer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.96 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.469, 101.395, 69.131, 90, 105.56, 90
R / Rfree (%) 17.8 / 20.2

Other elements in 7z76:

The structure of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb also contains other interesting chemical elements:

Bromine (Br) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb (pdb code 7z76). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb, PDB code: 7z76:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 1 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:24.1
occ:0.57
O C:HOH509 3.4 38.1 1.0
O C:HOH588 3.6 47.9 1.0
N C:PRO97 4.1 13.7 1.0
CG2 C:VAL87 4.2 13.6 1.0
CD C:PRO97 4.2 16.3 1.0
CG1 C:VAL87 4.2 14.2 1.0
CB C:PRO97 4.3 15.1 1.0
CB C:PRO95 4.3 16.3 1.0
C C:GLN96 4.4 15.6 1.0
CA C:PRO97 4.5 12.9 1.0
C C:PRO95 4.5 17.8 1.0
O C:PRO95 4.5 19.3 1.0
N C:GLN96 4.6 13.8 1.0
CD2 C:LEU85 4.6 16.0 1.0
CG C:PRO97 4.6 19.6 1.0
CA C:GLN96 4.7 13.7 1.0
CG2 C:VAL194 4.8 21.2 1.0
CG C:PRO95 4.8 18.8 1.0
CB C:VAL87 4.8 13.4 1.0
O C:GLN96 4.9 14.8 1.0
CE1 C:HIS125 5.0 27.2 1.0
O C:HOH452 5.0 30.6 1.0

Iodine binding site 2 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 2 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:15.9
occ:0.76
O C:HOH428 3.4 36.2 1.0
N C:ARG108 3.6 12.6 1.0
CA C:ARG107 4.1 13.6 1.0
CB C:ARG108 4.2 13.8 1.0
C C:ARG107 4.4 13.9 1.0
O C:GLY106 4.4 19.2 1.0
CG C:ARG107 4.6 16.2 1.0
CA C:ARG108 4.6 12.3 1.0
CB C:ARG107 4.9 14.4 1.0
O C:ARG108 5.0 15.3 1.0

Iodine binding site 3 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 3 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I303

b:16.7
occ:0.58
NE C:ARG107 4.0 15.4 1.0
CZ C:ARG107 4.0 18.0 1.0
C72 D:IFJ1501 4.0 16.5 1.0
NH1 C:ARG107 4.1 16.5 1.0
CD C:ARG107 4.2 15.8 1.0
NH2 C:ARG107 4.5 18.5 1.0

Iodine binding site 4 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 4 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I304

b:20.5
occ:0.37
O C:HOH495 2.9 21.4 1.0
ND1 C:HIS110 3.2 27.1 1.0
N C:HIS110 3.5 14.4 1.0
CA C:ILE109 3.9 12.9 1.0
CB C:HIS110 4.0 18.3 1.0
C58 D:IFJ1501 4.0 13.4 1.0
C59 D:IFJ1501 4.0 14.5 1.0
C66 D:IFJ1501 4.0 15.3 1.0
CG C:HIS110 4.0 23.9 1.0
C63 D:IFJ1501 4.1 13.0 1.0
C60 D:IFJ1501 4.1 13.1 1.0
C C:ILE109 4.2 15.5 1.0
C62 D:IFJ1501 4.2 13.8 1.0
C61 D:IFJ1501 4.2 13.4 1.0
CE1 C:HIS110 4.3 27.3 1.0
CA C:HIS110 4.4 14.9 1.0
CB C:ILE109 4.4 14.9 1.0
O C:ARG108 4.5 15.3 1.0
C65 D:IFJ1501 4.6 14.2 1.0
C72 D:IFJ1501 4.7 16.5 1.0
CG2 C:ILE109 4.8 15.0 1.0
O C:HIS110 5.0 16.2 1.0

Iodine binding site 5 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 5 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I1502

b:17.5
occ:0.87
O D:HOH1614 3.4 20.6 1.0
CG2 D:ILE1470 3.5 24.9 1.0
NE2 C:GLN96 3.6 16.7 1.0
O C:HOH462 3.6 25.0 1.0
N D:ILE1470 3.7 16.0 1.0
N D:GLN1469 4.0 16.5 1.0
CB D:ILE1470 4.0 20.8 1.0
C15 D:IFJ1501 4.0 16.0 1.0
CB D:SER1468 4.1 19.4 1.0
C28 D:IFJ1501 4.2 17.2 1.0
CB D:GLN1469 4.2 17.4 1.0
OE1 C:GLN96 4.3 17.6 1.0
C27 D:IFJ1501 4.4 16.4 1.0
CA D:GLN1469 4.4 16.5 1.0
OG D:SER1468 4.4 18.4 1.0
CD C:GLN96 4.4 19.4 1.0
CA D:ILE1470 4.5 16.2 1.0
C D:GLN1469 4.5 18.9 1.0
C D:SER1468 4.7 18.9 1.0
C16 D:IFJ1501 4.7 16.0 1.0
C14 D:IFJ1501 4.8 16.4 1.0
CZ3 C:TRP88 4.8 14.4 1.0
CA D:SER1468 4.9 17.6 1.0
C17 D:IFJ1501 4.9 17.4 1.0
OD1 D:ASN1464 5.0 18.2 1.0

Iodine binding site 6 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 6 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I1503

b:27.1
occ:0.42
O D:HOH1645 3.5 17.5 1.0
CD1 D:LEU1418 4.1 24.2 1.0
C66 D:IFJ1501 4.2 15.3 1.0
C65 D:IFJ1501 4.3 14.2 1.0
O67 D:IFJ1501 4.3 16.1 1.0
C31 D:IFJ1501 4.4 19.2 1.0
O D:HOH1767 4.4 47.7 1.0
C30 D:IFJ1501 4.4 19.0 1.0
C59 D:IFJ1501 4.6 14.5 1.0
C26 D:IFJ1501 4.7 18.0 1.0
N32 D:IFJ1501 4.7 18.6 1.0
C57 D:IFJ1501 4.9 18.8 1.0
C27 D:IFJ1501 4.9 16.4 1.0
C58 D:IFJ1501 4.9 13.4 1.0
CD2 D:LEU1418 5.0 25.9 1.0

Iodine binding site 7 out of 7 in 7z76

Go back to Iodine Binding Sites List in 7z76
Iodine binding site 7 out of 7 in the Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Compound 10 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I1504

b:40.4
occ:0.39
ND2 D:ASN1440 3.5 48.6 1.0
NZ D:LYS1442 3.6 57.6 1.0
CE D:LYS1442 3.9 63.2 1.0
CG D:GLU1436 3.9 41.1 1.0
CD D:GLU1436 4.1 69.8 1.0
OE1 D:GLU1436 4.1 69.3 1.0
CB D:ASN1440 4.1 35.0 1.0
CG D:ARG1437 4.2 30.6 1.0
O D:GLU1436 4.3 30.3 1.0
CG D:ASN1440 4.4 57.7 1.0
C D:GLU1436 4.4 30.5 1.0
CA D:ARG1437 4.4 27.0 1.0
N D:ARG1437 4.5 27.2 1.0
CB D:GLU1436 4.7 28.2 1.0
CD D:LYS1442 4.7 58.5 1.0
OE2 D:GLU1436 4.8 65.8 1.0
CB D:ARG1437 4.9 25.0 1.0

Reference:

C.Kofink, N.Trainor, B.Mair, S.Wohrle, M.Wurm, N.Mischerikow, M.J.Roy, G.Bader, P.Greb, G.Garavel, E.Diers, R.Mclennan, C.Whitworth, V.Vetma, K.Rumpel, M.Scharnweber, J.E.Fuchs, T.Gerstberger, Y.Cui, G.Gremel, P.Chetta, S.Hopf, N.Budano, J.Rinnenthal, G.Gmaschitz, M.Mayer, M.Koegl, A.Ciulli, H.Weinstabl, W.Farnaby. A Selective and Orally Bioavailable Vhl-Recruiting Protac Achieves SMARCA2 Degradation in Vivo. Nat Commun V. 13 5969 2022.
ISSN: ESSN 2041-1723
PubMed: 36216795
DOI: 10.1038/S41467-022-33430-6
Page generated: Fri Aug 8 23:54:32 2025

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