Chemical Components in the PDB

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9VI : Summary

Code

9VI

One-letter code

X

Molecule name

N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-6,7-dihydro-1H-indazol-1-yl]acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-6,7-dihydro-1H-indazol-1-yl]acetamide
OpenEye OEToolkits 2.0.7 ~{N}-[(1~{S})-2-[3,5-bis(fluoranyl)phenyl]-1-[3-[4-chloranyl-1-methyl-3-(methylsulfonylamino)indazol-7-yl]-4-oxidanylidene-pyrido[2,3-d]pyrimidin-2-yl]ethyl]-2-[3-(trifluoromethyl)-6,7-dihydroindazol-1-yl]ethanamide

Formula

C34 H27 Cl F5 N9 O4 S

Formal charge

0

Molecular weight

788.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CS(=O)(=O)Nc1nn(C)c2c1c(Cl)ccc2N1C(=O)c2cccnc2N=C1C(Cc1cc(F)cc(F)c1)NC(=O)Cn1nc(c2C=CCCc21)C(F)(F)F
SMILES CACTVS 3.385 Cn1nc(N[S](C)(=O)=O)c2c(Cl)ccc(N3C(=O)c4cccnc4N=C3[CH](Cc5cc(F)cc(F)c5)NC(=O)Cn6nc(c7C=CCCc67)C(F)(F)F)c12
SMILES OpenEye OEToolkits 2.0.7 Cn1c2c(ccc(c2c(n1)NS(=O)(=O)C)Cl)N3C(=O)c4cccnc4N=C3C(Cc5cc(cc(c5)F)F)NC(=O)Cn6c7c(c(n6)C(F)(F)F)C=CCC7
Canonical SMILES CACTVS 3.385 Cn1nc(N[S](C)(=O)=O)c2c(Cl)ccc(N3C(=O)c4cccnc4N=C3[C@H](Cc5cc(F)cc(F)c5)NC(=O)Cn6nc(c7C=CCCc67)C(F)(F)F)c12
Canonical SMILES OpenEye OEToolkits 2.0.7 Cn1c2c(ccc(c2c(n1)NS(=O)(=O)C)Cl)N3C(=O)c4cccnc4N=C3[C@H](Cc5cc(cc(c5)F)F)NC(=O)Cn6c7c(c(n6)C(F)(F)F)C=CCC7

IUPAC InChI

InChI=1S/C34H27ClF5N9O4S/c1-47-28-25(10-9-22(35)27(28)31(45-47)46-54(2,52)53)49-32(43-30-21(33(49)51)7-5-11-41-30)23(14-17-12-18(36)15-19(37)13-17)42-26(50)16-48-24-8-4-3-6-20(24)29(44-48)34(38,39)40/h3,5-7,9-13,15,23H,4,8,14,16H2,1-2H3,(H,42,50)(H,45,46)/t23-/m0/s1

IUPAC InChI key

ZBYBMYJJANJYNU-QHCPKHFHSA-N
9VI

wwPDB Information

Atom count

81 (54 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-10-29

Last modified at

2022-09-30

Status

Released

Obsoleted

Not Assigned



9VI : Atoms of Molecule

Total Number of Atoms: 81
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 -2.721 2.056 -0.909
2 C13 C C2 N Y N 0 -3.16 0.874 -2.944
3 C15 C C3 N Y N 0 -3.247 -0.308 -0.85
4 C17 C C4 N N N 0 -4.695 -1.808 0.304
5 C20 C C5 N Y N 0 -6.086 -3.487 1.541
6 C21 C C6 N Y N 0 -6.132 -4.687 2.229
7 C22 C C7 N Y N 0 -4.968 -5.42 2.405
8 C24 C C8 N Y N 0 -3.704 -3.862 1.264
9 C26 C C9 N N N 0 -2.406 -2.324 0.113
10 C28 C C10 N N N 0 -0.78 -2.601 -1.739
11 C01 C C11 N N N 0 -2.855 0.253 2.267
12 C04 C C12 N Y N 0 -2.399 3.096 0.069
13 C07 C C13 N N N 0 -0.211 4.875 1.708
14 C11 C C14 N Y N 0 -2.844 2.038 -2.303
15 C14 C C15 N Y N 0 -3.362 -0.298 -2.227
16 C19 C C16 N Y N 0 -4.852 -3.065 1.048
17 C27 C C17 S N N 0 -1.044 -1.923 -0.393
18 C29 C C18 N Y N 0 0.526 -2.106 -2.303
19 C30 C C19 N Y N 0 0.548 -0.988 -3.117
20 C31 C C20 N Y N 0 1.749 -0.529 -3.631
21 C33 C C21 N Y N 0 2.928 -1.19 -3.33
22 C34 C C22 N Y N 0 2.905 -2.309 -2.516
23 C36 C C23 N Y N 0 1.703 -2.766 -2.003
24 C38 C C24 N N N 0 1.158 -1.694 0.624
25 C40 C C25 N N N 0 2.209 -2.122 1.616
26 C46 C C29 N N N 0 2.791 0.606 3.151
27 C43 C C26 N Y N 0 5.35 -0.534 0.768
28 C44 C C27 N Y N 0 4.834 0.36 1.706
29 C45 C C28 N Y N 0 3.616 -0.127 2.126
30 C47 C C30 N N N 0 3.732 1.356 4.095
31 C48 C C31 N N N 0 4.82 2.087 3.368
32 C49 C C32 N N N 0 5.37 1.628 2.247
33 C50 C C33 N N N 0 6.668 -0.405 0.049
34 C54 C C34 N Y N 0 -2.924 0.874 -0.174
35 F32 F F1 N N N 0 1.771 0.563 -4.426
36 F35 F F2 N N N 0 4.054 -2.955 -2.222
37 F51 F F3 N N N 0 6.791 -1.435 -0.89
38 F52 F F4 N N N 0 6.723 0.831 -0.605
39 F53 F F5 N N N 0 7.714 -0.489 0.974
40 N02 N N1 N Y N 0 -2.74 1.189 1.147
41 N03 N N2 N Y N 0 -2.418 2.546 1.254
42 N05 N N3 N N N 0 -2.12 4.436 -0.214
43 N16 N N4 N N N 0 -3.454 -1.495 -0.135
44 N23 N N5 N Y N 0 -3.811 -5.006 1.933
45 N25 N N6 N N N 0 -2.513 -3.435 0.777
46 N37 N N7 N N N 0 -0.023 -2.34 0.571
47 N41 N N8 N Y N 0 3.391 -1.269 1.474
48 N42 N N9 N Y N 0 4.486 -1.512 0.628
49 O08 O O1 N N N 0 -2.834 5.305 1.944
50 O09 O O2 N N N 0 -1.574 6.735 0.366
51 O18 O O3 N N N 0 -5.646 -1.079 0.087
52 O39 O O4 N N N 0 1.376 -0.767 -0.128
53 S06 S S1 N N N 0 -1.772 5.488 1.017
54 CL12 CL CL1 N N N 0 -2.596 3.494 -3.216
55 H1 H H1 N N N 0 -3.253 0.865 -4.02
56 H2 H H2 N N N 0 -6.978 -2.897 1.389
57 H3 H H3 N N N 0 -7.069 -5.049 2.627
58 H4 H H4 N N N 0 -5.012 -6.355 2.943
59 H5 H H5 N N N 0 -0.73 -3.68 -1.599
60 H6 H H6 N N N 0 -1.589 -2.361 -2.431
61 H7 H H7 N N N 0 -1.884 -0.204 2.46
62 H8 H H8 N N N 0 -3.187 0.789 3.157
63 H9 H H9 N N N 0 -3.579 -0.523 2.02
64 H10 H H10 N N N 0 -0.35 3.856 2.07
65 H11 H H11 N N N 0 0.557 4.885 0.935
66 H12 H H12 N N N 0 0.096 5.515 2.535
67 H13 H H13 N N N 0 -3.61 -1.209 -2.751
68 H16 H H16 N N N 0 3.865 -0.833 -3.731
69 H14 H H14 N N N 0 -1.006 -0.841 -0.517
70 H15 H H15 N N N 0 -0.371 -0.473 -3.352
71 H17 H H17 N N N 0 1.685 -3.636 -1.363
72 H18 H H18 N N N 0 1.813 -2.029 2.627
73 H19 H H19 N N N 0 2.484 -3.16 1.427
74 H20 H H20 N N N 0 2.133 1.316 2.651
75 H21 H H21 N N N 0 2.194 -0.108 3.718
76 H22 H H22 N N N 0 3.151 2.074 4.673
77 H23 H H23 N N N 0 4.188 0.641 4.78
78 H24 H H24 N N N 0 5.172 3.025 3.771
79 H25 H H25 N N N 0 6.171 2.159 1.753
80 H26 H H26 N N N 0 -2.131 4.75 -1.132
81 H27 H H27 N N N 0 -0.197 -3.081 1.172



9VI : Chemical Bonds

Total Number of Bonds: 87
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F52 C50 F C sing 1.4 N N
2 C48 C49 C C doub 1.33 N N
3 C48 C47 C C sing 1.5 N N
4 C49 C44 C C sing 1.48 N N
5 F53 C50 F C sing 1.4 N N
6 C50 C43 C C sing 1.51 N N
7 C50 F51 C F sing 1.4 N N
8 C44 C43 C C sing 1.39 N Y
9 C44 C45 C C doub 1.38 N Y
10 C47 C46 C C sing 1.53 N N
11 C43 N42 C N doub 1.31 N Y
12 C46 C45 C C sing 1.51 N N
13 C45 N41 C N sing 1.33 N Y
14 N42 N41 N N sing 1.4 N Y
15 F32 C31 F C sing 1.35 N N
16 N41 C40 N C sing 1.46 N N
17 C31 C33 C C doub 1.38 N Y
18 C31 C30 C C sing 1.38 N Y
19 C40 C38 C C sing 1.51 N N
20 C33 C34 C C sing 1.38 N Y
21 C30 C29 C C doub 1.38 N Y
22 C38 O39 C O doub 1.21 N N
23 C38 N37 C N sing 1.35 N N
24 C34 F35 C F sing 1.35 N N
25 C34 C36 C C doub 1.38 N Y
26 N37 C27 N C sing 1.46 N N
27 C29 C36 C C sing 1.38 N Y
28 C29 C28 C C sing 1.51 N N
29 O08 S06 O S doub 1.42 N N
30 O09 S06 O S doub 1.42 N N
31 C27 C28 C C sing 1.53 N N
32 C27 C26 C C sing 1.51 N N
33 S06 N05 S N sing 1.66 N N
34 S06 C07 S C sing 1.81 N N
35 N05 C04 N C sing 1.4 N N
36 N03 C04 N C doub 1.31 N Y
37 N03 N02 N N sing 1.4 N Y
38 C04 C10 C C sing 1.46 N Y
39 C26 N25 C N doub 1.3 N N
40 C26 N16 C N sing 1.36 N N
41 C01 N02 C N sing 1.46 N N
42 N25 C24 N C sing 1.36 N N
43 N02 C54 N C sing 1.37 N Y
44 C10 C54 C C doub 1.41 N Y
45 C10 C11 C C sing 1.4 N Y
46 C54 C15 C C sing 1.4 N Y
47 CL12 C11 CL C sing 1.74 N N
48 C11 C13 C C doub 1.37 N Y
49 C15 N16 C N sing 1.4 N N
50 C15 C14 C C doub 1.38 N Y
51 N16 C17 N C sing 1.35 N N
52 C13 C14 C C sing 1.39 N Y
53 C24 N23 C N doub 1.33 N Y
54 C24 C19 C C sing 1.41 N Y
55 N23 C22 N C sing 1.32 N Y
56 C17 C19 C C sing 1.47 N N
57 C17 O18 C O doub 1.22 N N
58 C19 C20 C C doub 1.39 N Y
59 C22 C21 C C doub 1.39 N Y
60 C20 C21 C C sing 1.38 N Y
61 C13 H1 C H sing 1.08 N N
62 C20 H2 C H sing 1.08 N N
63 C21 H3 C H sing 1.08 N N
64 C22 H4 C H sing 1.08 N N
65 C28 H5 C H sing 1.09 N N
66 C28 H6 C H sing 1.09 N N
67 C01 H7 C H sing 1.09 N N
68 C01 H8 C H sing 1.09 N N
69 C01 H9 C H sing 1.09 N N
70 C07 H10 C H sing 1.09 N N
71 C07 H11 C H sing 1.09 N N
72 C07 H12 C H sing 1.09 N N
73 C14 H13 C H sing 1.08 N N
74 C27 H14 C H sing 1.09 N N
75 C30 H15 C H sing 1.08 N N
76 C33 H16 C H sing 1.08 N N
77 C36 H17 C H sing 1.08 N N
78 C40 H18 C H sing 1.09 N N
79 C40 H19 C H sing 1.09 N N
80 C46 H20 C H sing 1.09 N N
81 C46 H21 C H sing 1.09 N N
82 C47 H22 C H sing 1.09 N N
83 C47 H23 C H sing 1.09 N N
84 C48 H24 C H sing 1.08 N N
85 C49 H25 C H sing 1.08 N N
86 N05 H26 N H sing 0.97 N N
87 N37 H27 N H sing 0.97 N N



9VI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9VI 7snl Open in New Window Bound ligand 1 1