Chemical Components in the PDB

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VKD : Summary

Code

VKD

One-letter code

X

Molecule name

Cobimetinib

Synonyms

{3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}{3-hydroxy-3-[(2R)-piperidin-2-yl]azetidin-1-yl}methanone

Systematic names

ProgramVersionName
ACDLabs 12.01 {3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}{3-hydroxy-3-[(2R)-piperidin-2-yl]azetidin-1-yl}methanone
OpenEye OEToolkits 2.0.7 [3,4-bis(fluoranyl)-2-[(2-fluoranyl-4-iodanyl-phenyl)amino]phenyl]-[3-oxidanyl-3-[(2~{R})-piperidin-2-yl]azetidin-1-yl]methanone

Formula

C21 H21 F3 I N3 O2

Formal charge

0

Molecular weight

531.31 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1CCCNC1C4(CN(C(c2c(c(c(cc2)F)F)Nc3ccc(I)cc3F)=O)C4)O
SMILES CACTVS 3.385 OC1(CN(C1)C(=O)c2ccc(F)c(F)c2Nc3ccc(I)cc3F)[CH]4CCCCN4
SMILES OpenEye OEToolkits 2.0.7 c1cc(c(cc1I)F)Nc2c(ccc(c2F)F)C(=O)N3CC(C3)(C4CCCCN4)O
Canonical SMILES CACTVS 3.385 OC1(CN(C1)C(=O)c2ccc(F)c(F)c2Nc3ccc(I)cc3F)[C@H]4CCCCN4
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(c(cc1I)F)Nc2c(ccc(c2F)F)C(=O)N3CC(C3)([C@H]4CCCCN4)O

IUPAC InChI

InChI=1S/C21H21F3IN3O2/c22-14-6-5-13(19(18(14)24)27-16-7-4-12(25)9-15(16)23)20(29)28-10-21(30,11-28)17-3-1-2-8-26-17/h4-7,9,17,26-27,30H,1-3,8,10-11H2/t17-/m1/s1

IUPAC InChI key

BSMCAPRUBJMWDF-QGZVFWFLSA-N
VKD

wwPDB Information

Atom count

51 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-08-21

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



VKD : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C25 C C1 N N N 0 -6.485 2.672 -0.283
2 C26 C C2 N N N 0 -7.595 3.351 0.525
3 C27 C C3 N N N 0 -8.759 2.372 0.701
4 N29 N N1 N N N 0 -7.194 0.492 0.581
5 C30 C C4 N N N 0 -4.127 -0.319 0.432
6 C10 C C5 N Y N 0 -0.087 -2.122 -0.513
7 C12 C C6 N Y N 0 1.841 -0.733 -0.943
8 C13 C C7 N Y N 0 2.173 -0.768 0.405
9 C14 C C8 N Y N 0 3.284 -0.084 0.86
10 C15 C C9 N Y N 0 4.065 0.637 -0.025
11 C17 C C10 N Y N 0 3.739 0.675 -1.369
12 C18 C C11 N Y N 0 2.628 -0.007 -1.831
13 C02 C C12 N N N 0 -1.72 -0.237 -0.562
14 C03 C C13 N Y N 0 -1.3 -1.564 -0.078
15 C04 C C14 N Y N 0 -2.107 -2.273 0.817
16 C05 C C15 N Y N 0 -1.711 -3.513 1.266
17 C06 C C16 N Y N 0 -0.512 -4.065 0.836
18 C08 C C17 N Y N 0 0.298 -3.375 -0.05
19 C21 C C18 N N N 0 -3.648 1.517 -0.481
20 C22 C C19 N N N 0 -4.95 0.702 -0.375
21 C24 C C20 R N N 0 -6.045 1.395 0.438
22 C28 C C21 N N N 0 -8.253 1.104 1.393
23 F07 F F1 N N N 0 -0.133 -5.282 1.284
24 F09 F F2 N N N 0 1.463 -3.919 -0.464
25 F19 F F3 N N N 0 2.309 0.031 -3.143
26 I16 I I1 N N N 0 5.747 1.673 0.671
27 N11 N N2 N N N 0 0.72 -1.429 -1.408
28 N20 N N3 N N N 0 -2.945 0.234 -0.258
29 O01 O O1 N N N 0 -0.961 0.432 -1.237
30 O23 O O2 N N N 0 -5.419 0.201 -1.628
31 H1 H H1 N N N 0 -6.859 2.419 -1.275
32 H2 H H2 N N N 0 -5.636 3.349 -0.375
33 H3 H H3 N N N 0 -7.21 3.639 1.503
34 H4 H H4 N N N 0 -7.941 4.237 -0.007
35 H5 H H5 N N N 0 -9.535 2.835 1.311
36 H6 H H6 N N N 0 -9.169 2.114 -0.276
37 H7 H H7 N N N 0 -7.546 0.21 -0.321
38 H9 H H9 N N N 0 -4.134 -0.137 1.507
39 H10 H H10 N N N 0 -4.34 -1.356 0.175
40 H11 H H11 N N N 0 1.564 -1.33 1.097
41 H12 H H12 N N N 0 3.542 -0.112 1.908
42 H13 H H13 N N N 0 4.351 1.239 -2.057
43 H14 H H14 N N N 0 -3.04 -1.849 1.155
44 H15 H H15 N N N 0 -2.336 -4.058 1.957
45 H16 H H16 N N N 0 -3.477 1.945 -1.469
46 H17 H H17 N N N 0 -3.513 2.238 0.325
47 H18 H H18 N N N 0 -5.658 1.65 1.425
48 H19 H H19 N N N 0 -7.856 1.361 2.375
49 H20 H H20 N N N 0 -9.077 0.4 1.507
50 H21 H H21 N N N 0 0.507 -1.429 -2.354
51 H22 H H22 N N N 0 -4.746 -0.266 -2.142



VKD : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C25 C26 C C sing 1.53 N N
2 C25 C24 C C sing 1.53 N N
3 C26 C27 C C sing 1.53 N N
4 C27 C28 C C sing 1.53 N N
5 C24 N29 C N sing 1.47 N N
6 C24 C22 C C sing 1.53 N N
7 C21 C22 C C sing 1.54 N N
8 C21 N20 C N sing 1.48 N N
9 N29 C28 N C sing 1.47 N N
10 C22 O23 C O sing 1.43 N N
11 C22 C30 C C sing 1.54 N N
12 O01 C02 O C doub 1.22 N N
13 N20 C02 N C sing 1.35 N N
14 N20 C30 N C sing 1.48 N N
15 C02 C03 C C sing 1.47 N N
16 F19 C18 F C sing 1.35 N N
17 C03 C04 C C doub 1.4 N Y
18 C03 C10 C C sing 1.4 N Y
19 N11 C10 N C sing 1.39 N N
20 N11 C12 N C sing 1.4 N N
21 C04 C05 C C sing 1.38 N Y
22 C18 C12 C C doub 1.39 N Y
23 C18 C17 C C sing 1.38 N Y
24 C10 C08 C C doub 1.39 N Y
25 C12 C13 C C sing 1.39 N Y
26 C17 C15 C C doub 1.38 N Y
27 C05 C06 C C doub 1.39 N Y
28 C08 C06 C C sing 1.38 N Y
29 C08 F09 C F sing 1.35 N N
30 C06 F07 C F sing 1.35 N N
31 C13 C14 C C doub 1.38 N Y
32 C15 C14 C C sing 1.38 N Y
33 C15 I16 C I sing 2.09 N N
34 C25 H1 C H sing 1.09 N N
35 C25 H2 C H sing 1.09 N N
36 C26 H3 C H sing 1.09 N N
37 C26 H4 C H sing 1.09 N N
38 C27 H5 C H sing 1.09 N N
39 C27 H6 C H sing 1.09 N N
40 N29 H7 N H sing 1.01 N N
41 C30 H9 C H sing 1.09 N N
42 C30 H10 C H sing 1.09 N N
43 C13 H11 C H sing 1.08 N N
44 C14 H12 C H sing 1.08 N N
45 C17 H13 C H sing 1.08 N N
46 C04 H14 C H sing 1.08 N N
47 C05 H15 C H sing 1.08 N N
48 C21 H16 C H sing 1.09 N N
49 C21 H17 C H sing 1.09 N N
50 C24 H18 C H sing 1.09 N N
51 C28 H19 C H sing 1.09 N N
52 C28 H20 C H sing 1.09 N N
53 N11 H21 N H sing 0.97 N N
54 O23 H22 O H sing 0.97 N N



VKD : Used in PDB Entries

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