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Iodine in PDB 3vqu: Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide

Enzymatic activity of Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide

All present enzymatic activity of Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide:
2.7.12.1;

Protein crystallography data

The structure of Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide, PDB code: 3vqu was solved by K.Kusakabe, N.Ide, Y.Daigo, T.Itoh, K.Higashino, Y.Okano, G.Tadano, Y.Tachibana, Y.Sato, M.Inoue, T.Wada, M.Iguchi, T.Kanazawa, Y.Ishioka, K.Dohi, S.Tagashira, Y.Kido, S.Sakamoto, K.Yasuo, M.Maeda, T.Yamamoto, M.Higaki, T.Endoh, K.Ueda, T.Shiota, H.Murai, Y.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.470, 106.070, 112.080, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 28.4

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide (pdb code 3vqu). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide, PDB code: 3vqu:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 1 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I901

b:78.6
occ:0.60
 OD1 A:ASP657 3.6 62.4 1.0
N A:ASP657 3.7 56.6 1.0
CG1 A:VAL656 4.0 55.3 1.0
CB A:ASN606 4.1 52.0 1.0
N A:ASN606 4.1 48.9 1.0
C A:GLY605 4.2 47.5 1.0
ND2 A:ASN606 4.2 60.9 1.0
CA A:VAL656 4.3 53.3 1.0
I A:IOD907 4.4 79.1 0.4
CA A:ASN606 4.4 50.7 1.0
O A:GLY605 4.4 47.6 1.0
C A:VAL656 4.5 55.2 1.0
CA A:ASP657 4.5 57.6 1.0
CA A:GLY605 4.6 45.5 1.0
CG A:ASP657 4.6 61.0 1.0
CG A:ASN606 4.6 55.5 1.0
O A:HOH1120 4.8 56.8 1.0
CB A:VAL656 4.8 53.2 1.0
O A:ILE655 4.9 47.2 1.0

Iodine binding site 2 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 2 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I902

b:65.9
occ:0.64
 N A:GLN670 3.7 65.1 1.0
CB A:ASN669 3.8 61.0 1.0
CA A:ASN669 3.9 61.7 1.0
C A:ASN669 4.3 63.6 1.0
CG A:ASN669 4.4 62.3 1.0
OD1 A:ASN669 4.5 65.9 1.0
O A:GLN670 4.7 70.5 1.0
CA A:GLN670 4.7 68.3 1.0
CB A:GLN670 4.8 67.8 1.0

Iodine binding site 3 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 3 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I903

b:41.5
occ:1.00
 CB A:PRO713 3.6 42.4 1.0
N A:ILE782 3.6 37.0 1.0
O A:HOH1104 3.7 45.8 1.0
C A:PRO713 3.8 41.0 1.0
CG1 A:ILE782 3.9 38.6 1.0
O A:PRO713 3.9 41.0 1.0
N A:LYS714 4.0 39.3 1.0
CB A:SER781 4.1 39.7 1.0
CA A:SER781 4.1 39.2 1.0
ND1 A:HIS639 4.1 37.7 1.0
CG2 A:VAL717 4.1 31.0 1.0
CB A:ILE782 4.2 36.7 1.0
CE1 A:HIS639 4.2 34.5 1.0
CD A:LYS714 4.3 40.0 1.0
CA A:LYS714 4.3 39.1 1.0
CA A:PRO713 4.4 42.5 1.0
C A:SER781 4.4 37.4 1.0
CA A:ILE782 4.5 36.5 1.0
CE A:LYS714 4.6 41.4 1.0
CG A:LYS714 4.7 39.7 1.0
CG A:PRO713 4.7 45.1 1.0
CD A:PRO783 4.7 37.1 1.0

Iodine binding site 4 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 4 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I904

b:72.6
occ:0.50
 N A:GLN736 4.0 61.9 1.0
CG A:GLN735 4.0 60.1 1.0
CD A:LYS731 4.1 64.7 1.0
CA A:GLN736 4.1 62.4 1.0
CB A:GLN735 4.1 60.0 1.0
NE2 A:GLN735 4.2 61.8 1.0
CB A:GLN736 4.3 62.1 1.0
C A:GLN735 4.4 61.0 1.0
CD A:GLN735 4.4 61.2 1.0
NE2 A:GLN736 4.6 66.3 1.0
O A:GLN735 4.8 60.8 1.0
CB A:LYS731 4.8 56.9 1.0
NZ A:LYS731 4.8 67.9 1.0
CA A:GLN735 4.9 60.2 1.0
CG A:LYS731 4.9 59.4 1.0

Iodine binding site 5 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 5 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I905

b:72.7
occ:0.44
 N A:ASP775 3.6 50.9 1.0
CG A:LYS773 3.7 53.6 1.0
CB A:ASP775 3.7 51.6 1.0
N A:ARG774 3.9 51.2 1.0
CB A:LYS773 4.2 49.7 1.0
CB A:GLN778 4.2 51.8 1.0
CA A:ASP775 4.3 50.9 1.0
CG A:GLN778 4.3 57.1 1.0
CA A:LYS773 4.4 51.0 1.0
C A:LYS773 4.4 51.6 1.0
CA A:ARG774 4.6 51.5 1.0
C A:ARG774 4.6 51.2 1.0
CB A:ARG774 4.6 51.4 1.0
O A:ASP775 4.7 49.6 1.0

Iodine binding site 6 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 6 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I906

b:72.2
occ:0.45
 C A:ILE759 3.6 60.1 1.0
CA A:ILE759 3.8 60.4 1.0
N A:PRO760 3.8 59.7 1.0
N A:ILE759 3.8 61.9 1.0
O A:ILE759 4.0 61.4 1.0
C A:ASP758 4.0 63.3 1.0
O A:ASP758 4.1 62.7 1.0
CD A:PRO760 4.1 59.7 1.0
CB A:ASP758 4.2 65.7 1.0
NZ A:LYS762 4.4 66.4 1.0
CA A:PRO760 4.5 60.1 1.0
CG A:PRO760 4.7 60.4 1.0
CA A:ASP758 4.8 64.5 1.0

Iodine binding site 7 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 7 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


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 Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I907

b:79.1
occ:0.42
 O A:HOH1102 2.8 55.5 1.0
N A:GLY605 3.1 44.0 1.0
CA A:GLY605 3.6 45.5 1.0
CG1 A:VAL656 3.9 55.3 1.0
O A:GLY605 3.9 47.6 1.0
N A:CYS604 4.0 43.7 1.0
C A:CYS604 4.1 43.6 1.0
C A:GLY605 4.1 47.5 1.0
CG A:GLU603 4.3 49.4 1.0
CB A:CYS604 4.3 44.8 1.0
CA A:CYS604 4.4 44.0 1.0
I A:IOD901 4.4 78.6 0.6
CG2 A:ILE549 4.5 41.1 1.0
OE2 A:GLU603 4.8 58.0 1.0

Iodine binding site 8 out of 8 in 3vqu

Go back to Iodine Binding Sites List in 3vqu
Iodine binding site 8 out of 8 in the Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Human MPS1 Catalytic Domain in Complex with 4- [(4-Amino-5-Cyano-6-Ethoxypyridin-2- Yl)Amino]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I908

b:93.1
occ:0.50
 C A:SER536 4.0 62.8 1.0
O A:SER536 4.0 62.4 1.0
CE2 A:TYR554 4.0 50.5 1.0
CA A:SER536 4.0 63.7 1.0
CB A:ASN556 4.1 53.6 1.0
CD A:LYS538 4.3 59.7 1.0
ND2 A:ASN556 4.5 58.5 1.0
N A:SER537 4.5 61.3 1.0
CD2 A:TYR554 4.5 48.0 1.0
CB A:SER536 4.8 63.9 1.0
CG A:ASN556 4.9 56.3 1.0
CG A:LYS538 4.9 58.2 1.0
CZ A:TYR554 5.0 49.7 1.0

Reference:

K.Kusakabe, N.Ide, Y.Daigo, T.Itoh, K.Higashino, Y.Okano, G.Tadano, Y.Tachibana, Y.Sato, M.Inoue, T.Wada, M.Iguchi, T.Kanazawa, Y.Ishioka, K.Dohi, S.Tagashira, Y.Kido, S.Sakamoto, K.Yasuo, M.Maeda, T.Yamamoto, M.Higaki, T.Endoh, K.Ueda, T.Shiota, H.Murai, Y.Nakamura. Diaminopyridine-Based Potent and Selective MPS1 Kinase Inhibitors Binding to An Unusual Flipped-Peptide Conformation. Acs Med.Chem.Lett. V. 3 560 2012.
ISSN: ISSN 1948-5875
PubMed: 24900510
DOI: 10.1021/ML3000879
Page generated: Sun Jan 24 17:26:50 2021

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