Chemical Components in the PDB

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VGH : Summary

Code

VGH

One-letter code

X

Molecule name

3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine

Synonyms

CRIZOTINIB

Systematic names

ProgramVersionName
ACDLabs 10.04 3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
OpenEye OEToolkits 1.6.1 3-[(1R)-1-(2,6-dichloro-3-fluoro-phenyl)ethoxy]-5-(1-piperidin-4-ylpyrazol-4-yl)pyridin-2-amine

Formula

C21 H22 Cl2 F N5 O

Formal charge

0

Molecular weight

450.337 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Clc1ccc(F)c(Cl)c1C(Oc2cc(cnc2N)c3cnn(c3)C4CCNCC4)C
SMILES CACTVS 3.352 C[CH](Oc1cc(cnc1N)c2cnn(c2)C3CCNCC3)c4c(Cl)ccc(F)c4Cl
SMILES OpenEye OEToolkits 1.6.1 CC(c1c(ccc(c1Cl)F)Cl)Oc2cc(cnc2N)c3cnn(c3)C4CCNCC4
Canonical SMILES CACTVS 3.352 C[C@@H](Oc1cc(cnc1N)c2cnn(c2)C3CCNCC3)c4c(Cl)ccc(F)c4Cl
Canonical SMILES OpenEye OEToolkits 1.6.1 C[C@H](c1c(ccc(c1Cl)F)Cl)Oc2cc(cnc2N)c3cnn(c3)C4CCNCC4

IUPAC InChI

InChI=1S/C21H22Cl2FN5O/c1-12(19-16(22)2-3-17(24)20(19)23)30-18-8-13(9-27-21(18)25)14-10-28-29(11-14)15-4-6-26-7-5-15/h2-3,8-12,15,26H,4-7H2,1H3,(H2,25,27)/t12-/m1/s1

IUPAC InChI key

KTEIFNKAUNYNJU-GFCCVEGCSA-N
VGH

wwPDB Information

Atom count

52 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-04-20

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



VGH : Atoms of Molecule

Total Number of Atoms: 52
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CL CL CL N N N 0 2.709 3.05 0.802
2 C13 C C13 N Y N 0 4.031 1.971 0.487
3 C3 C C3 N Y N 0 5.322 2.343 0.82
4 C2 C C2 N Y N 0 6.376 1.484 0.57
5 C12 C C12 N Y N 0 6.14 0.251 -0.014
6 F F F N N N 0 7.17 -0.589 -0.258
7 C17 C C17 N Y N 0 3.794 0.737 -0.091
8 C18 C C18 N Y N 0 4.848 -0.121 -0.347
9 CL2 CL CL2 N N N 0 4.551 -1.667 -1.079
10 C21 C C21 R N N 0 2.387 0.33 -0.447
11 C1 C C1 N N N 0 2.196 0.428 -1.962
12 O27 O O27 N N N 0 2.159 -1.016 -0.025
13 C15 C C15 N Y N 0 0.872 -1.375 0.227
14 C4 C C4 N Y N 0 -0.165 -0.494 -0.032
15 C19 C C19 N Y N 0 0.578 -2.637 0.746
16 N22 N N22 N N N 0 1.612 -3.533 1.006
17 N23 N N23 N Y N 0 -0.672 -2.993 0.993
18 C5 C C5 N Y N 0 -1.685 -2.18 0.763
19 C14 C C14 N Y N 0 -1.473 -0.908 0.243
20 C16 C C16 N Y N 0 -2.62 -0.0010 -0.017
21 C6 C C6 N Y N 0 -2.546 1.305 -0.539
22 C7 C C7 N Y N 0 -3.936 -0.283 0.2
23 N26 N N26 N Y N 0 -4.652 0.801 -0.164
24 N24 N N24 N Y N 0 -3.761 1.779 -0.622
25 C20 C C20 N N N 0 -6.109 0.931 -0.095
26 C8 C C8 N N N 0 -6.736 0.339 -1.36
27 C10 C C10 N N N 0 -8.26 0.423 -1.256
28 N25 N N25 N N N 0 -8.712 -0.318 -0.071
29 C11 C C11 N N N 0 -8.161 0.262 1.16
30 C9 C C9 N N N 0 -6.634 0.173 1.128
31 H3 H H3 N N N 0 5.506 3.305 1.274
32 H2 H H2 N N N 0 7.383 1.775 0.829
33 H21 H H21 N N N 0 1.68 0.992 0.052
34 H11C H H11C N N N 0 2.37 1.455 -2.284
35 H12C H H12C N N N 0 2.903 -0.234 -2.461
36 H13C H H13C N N N 0 1.179 0.134 -2.22
37 H4 H H4 N N N 0 0.031 0.488 -0.437
38 H221 H H221 N N N 0 2.531 -3.277 0.827
39 H222 H H222 N N N 0 1.414 -4.411 1.366
40 H5 H H5 N N N 0 -2.692 -2.507 0.977
41 H6 H H6 N N N 0 -1.642 1.825 -0.822
42 H7 H H7 N N N 0 -4.334 -1.207 0.593
43 H20 H H20 N N N 0 -6.377 1.985 -0.014
44 H81C H H81C N N N 0 -6.399 0.902 -2.231
45 H82C H H82C N N N 0 -6.435 -0.704 -1.462
46 H91C H H91C N N N 0 -6.331 -0.872 1.065
47 H92C H H92C N N N 0 -6.224 0.618 2.035
48 H101 H H101 N N N 0 -8.562 1.467 -1.168
49 H102 H H102 N N N 0 -8.71 -0.011 -2.149
50 H25 H H25 N N N 0 -9.72 -0.358 -0.032
51 H111 H H111 N N N 0 -8.463 1.306 1.237
52 H112 H H112 N N N 0 -8.538 -0.289 2.022



VGH : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CL C13 CL C sing 1.74 N N
2 C13 C3 C C sing 1.38 N Y
3 C13 C17 C C doub 1.38 N Y
4 C3 C2 C C doub 1.38 N Y
5 C2 C12 C C sing 1.38 N Y
6 C12 F C F sing 1.35 N N
7 C12 C18 C C doub 1.39 N Y
8 C17 C18 C C sing 1.38 N Y
9 C17 C21 C C sing 1.51 N N
10 C18 CL2 C CL sing 1.74 N N
11 C21 C1 C C sing 1.53 N N
12 C21 O27 C O sing 1.43 N N
13 O27 C15 O C sing 1.36 N N
14 C15 C4 C C doub 1.39 N Y
15 C15 C19 C C sing 1.4 N Y
16 C4 C14 C C sing 1.4 N Y
17 C19 N22 C N sing 1.39 N N
18 C19 N23 C N doub 1.32 N Y
19 N23 C5 N C sing 1.32 N Y
20 C5 C14 C C doub 1.39 N Y
21 C14 C16 C C sing 1.49 N Y
22 C16 C6 C C sing 1.41 N Y
23 C16 C7 C C doub 1.36 N Y
24 C6 N24 C N doub 1.31 N Y
25 C7 N26 C N sing 1.35 N Y
26 N26 N24 N N sing 1.4 N Y
27 N26 C20 N C sing 1.46 N N
28 C20 C8 C C sing 1.53 N N
29 C20 C9 C C sing 1.53 N N
30 C8 C10 C C sing 1.53 N N
31 C10 N25 C N sing 1.47 N N
32 N25 C11 N C sing 1.47 N N
33 C11 C9 C C sing 1.53 N N
34 C3 H3 C H sing 1.08 N N
35 C2 H2 C H sing 1.08 N N
36 C21 H21 C H sing 1.09 N N
37 C1 H11C C H sing 1.09 N N
38 C1 H12C C H sing 1.09 N N
39 C1 H13C C H sing 1.09 N N
40 C4 H4 C H sing 1.08 N N
41 N22 H221 N H sing 0.97 N N
42 N22 H222 N H sing 0.97 N N
43 C5 H5 C H sing 1.08 N N
44 C6 H6 C H sing 1.08 N N
45 C7 H7 C H sing 1.08 N N
46 C20 H20 C H sing 1.09 N N
47 C8 H81C C H sing 1.09 N N
48 C8 H82C C H sing 1.09 N N
49 C9 H91C C H sing 1.09 N N
50 C9 H92C C H sing 1.09 N N
51 C10 H101 C H sing 1.09 N N
52 C10 H102 C H sing 1.09 N N
53 N25 H25 N H sing 1.01 N N
54 C11 H111 C H sing 1.09 N N
55 C11 H112 C H sing 1.09 N N



VGH : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
VGH 2wgj Open in New Window Bound ligand 1 1
VGH 2xp2 Open in New Window Bound ligand 1 1
VGH 2yfx Open in New Window Bound ligand 1 1
VGH 3zbf Open in New Window Bound ligand 1 1
VGH 4anq Open in New Window Bound ligand 1 1
VGH 4ans Open in New Window Bound ligand 1 1
VGH 4c9w Open in New Window Bound ligand 1 1
VGH 5aaa Open in New Window Bound ligand 1 1
VGH 5aab Open in New Window Bound ligand 1 1
VGH 5aac Open in New Window Bound ligand 1 1
VGH 6imz Open in New Window Bound ligand 1 1