Chemical Components in the PDB

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XL5 : Summary

Code

XL5

One-letter code

X

Molecule name

N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide
OpenEye OEToolkits 2.0.6 ~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-fluoranyl-phenyl]propanamide

Formula

C22 H21 Cl2 F N4 O4

Formal charge

0

Molecular weight

495.331 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1(c(c(c(Cl)c(OC)c1)COc3cnc(Nc2c(cccc2NC(CC)=O)F)nc3)Cl)OC
SMILES CACTVS 3.385 CCC(=O)Nc1cccc(F)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2
SMILES OpenEye OEToolkits 2.0.6 CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)F
Canonical SMILES CACTVS 3.385 CCC(=O)Nc1cccc(F)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2
Canonical SMILES OpenEye OEToolkits 2.0.6 CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)F

IUPAC InChI

InChI=1S/C22H21Cl2FN4O4/c1-4-18(30)28-15-7-5-6-14(25)21(15)29-22-26-9-12(10-27-22)33-11-13-19(23)16(31-2)8-17(32-3)20(13)24/h5-10H,4,11H2,1-3H3,(H,28,30)(H,26,27,29)

IUPAC InChI key

QQZLOGCMIZJHHI-UHFFFAOYSA-N
XL5

wwPDB Information

Atom count

54 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-11-05

Last modified at

2019-07-05

Status

Released

Obsoleted

Not Assigned



XL5 : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 5.954 -0.756 0.212
2 C2 C C2 N Y N 0 4.589 -0.984 0.105
3 C3 C C3 N Y N 0 3.745 0.037 -0.29
4 C4 C C4 N Y N 0 4.258 1.288 -0.58
5 C5 C C5 N Y N 0 5.623 1.52 -0.474
6 C6 C C6 N Y N 0 6.471 0.498 -0.078
7 O1 O O1 N N N 0 6.783 -1.759 0.605
8 O2 O O2 N N N 0 6.127 2.75 -0.759
9 C7 C C7 N N N 0 8.176 -1.452 0.693
10 C8 C C8 N N N 0 7.54 2.918 -0.628
11 CL1 CL CL1 N N N 0 3.941 -2.554 0.468
12 CL2 CL CL2 N N N 0 3.196 2.568 -1.076
13 C9 C C9 N N N 0 2.263 -0.214 -0.407
14 O3 O O3 N N N 0 1.632 0.071 0.844
15 C10 C C10 N Y N 0 0.285 -0.105 0.91
16 C11 C C11 N Y N 0 -0.408 0.149 2.088
17 N1 N N1 N Y N 0 -1.718 -0.033 2.116
18 C12 C C12 N Y N 0 -2.368 -0.452 1.041
19 N2 N N2 N Y N 0 -1.74 -0.703 -0.098
20 C13 C C13 N Y N 0 -0.431 -0.537 -0.2
21 N3 N N3 N N N 0 -3.741 -0.632 1.109
22 C14 C C14 N Y N 0 -4.463 -0.958 -0.047
23 C15 C C15 N Y N 0 -5.503 -0.135 -0.478
24 C16 C C16 N Y N 0 -6.213 -0.463 -1.624
25 C17 C C17 N Y N 0 -5.89 -1.603 -2.335
26 C18 C C18 N Y N 0 -4.86 -2.421 -1.909
27 C19 C C19 N Y N 0 -4.142 -2.099 -0.771
28 N4 N N4 N N N 0 -5.829 1.021 0.244
29 C20 C C20 N N N 0 -7.111 1.431 0.315
30 C21 C C21 N N N 0 -7.478 2.609 1.18
31 C22 C C22 N N N 0 -8.983 2.864 1.083
32 O4 O O4 N N N 0 -7.969 0.852 -0.317
33 F1 F F1 N N N 0 -3.132 -2.897 -0.36
34 H1 H H1 N N N 0 7.532 0.677 0.004
35 H2 H H2 N N N 0 8.723 -2.338 1.017
36 H3 H H3 N N N 0 8.541 -1.137 -0.285
37 H4 H H4 N N N 0 8.326 -0.648 1.413
38 H5 H H5 N N N 0 7.81 3.942 -0.885
39 H6 H H6 N N N 0 7.838 2.71 0.4
40 H7 H H7 N N N 0 8.052 2.229 -1.301
41 H8 H H8 N N N 0 1.845 0.431 -1.18
42 H9 H H9 N N N 0 2.091 -1.257 -0.671
43 H10 H H10 N N N 0 0.116 0.49 2.969
44 H11 H H11 N N N 0 0.075 -0.744 -1.131
45 H12 H H12 N N N 0 -4.202 -0.532 1.956
46 H13 H H13 N N N 0 -7.019 0.173 -1.959
47 H14 H H14 N N N 0 -6.445 -1.857 -3.226
48 H15 H H15 N N N 0 -4.612 -3.311 -2.469
49 H16 H H16 N N N 0 -5.133 1.525 0.692
50 H17 H H17 N N N 0 -7.211 2.397 2.216
51 H18 H H18 N N N 0 -6.937 3.492 0.84
52 H19 H H19 N N N 0 -9.248 3.716 1.709
53 H20 H H20 N N N 0 -9.25 3.076 0.048
54 H21 H H21 N N N 0 -9.524 1.981 1.424



XL5 : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 C21 C C sing 1.53 N N
2 C21 C20 C C sing 1.51 N N
3 O4 C20 O C doub 1.21 N N
4 C20 N4 C N sing 1.35 N N
5 CL1 C2 CL C sing 1.74 N N
6 C7 O1 C O sing 1.43 N N
7 N4 C15 N C sing 1.4 N N
8 O1 C1 O C sing 1.36 N N
9 C13 N2 C N doub 1.32 N Y
10 C13 C10 C C sing 1.39 N Y
11 C1 C2 C C doub 1.39 N Y
12 C1 C6 C C sing 1.39 N Y
13 C2 C3 C C sing 1.38 N Y
14 N2 C12 N C sing 1.32 N Y
15 O3 C10 O C sing 1.36 N N
16 O3 C9 O C sing 1.43 N N
17 C10 C11 C C doub 1.39 N Y
18 C15 C16 C C doub 1.39 N Y
19 C15 C14 C C sing 1.39 N Y
20 C12 N3 C N sing 1.39 N N
21 C12 N1 C N doub 1.32 N Y
22 N3 C14 N C sing 1.4 N N
23 C11 N1 C N sing 1.32 N Y
24 C6 C5 C C doub 1.39 N Y
25 C9 C3 C C sing 1.51 N N
26 C3 C4 C C doub 1.38 N Y
27 C16 C17 C C sing 1.38 N Y
28 C14 C19 C C doub 1.39 N Y
29 C5 C4 C C sing 1.39 N Y
30 C5 O2 C O sing 1.36 N N
31 C4 CL2 C CL sing 1.74 N N
32 C8 O2 C O sing 1.43 N N
33 C17 C18 C C doub 1.38 N Y
34 C19 C18 C C sing 1.38 N Y
35 C19 F1 C F sing 1.35 N N
36 C6 H1 C H sing 1.08 N N
37 C7 H2 C H sing 1.09 N N
38 C7 H3 C H sing 1.09 N N
39 C7 H4 C H sing 1.09 N N
40 C8 H5 C H sing 1.09 N N
41 C8 H6 C H sing 1.09 N N
42 C8 H7 C H sing 1.09 N N
43 C9 H8 C H sing 1.09 N N
44 C9 H9 C H sing 1.09 N N
45 C11 H10 C H sing 1.08 N N
46 C13 H11 C H sing 1.08 N N
47 N3 H12 N H sing 0.97 N N
48 C16 H13 C H sing 1.08 N N
49 C17 H14 C H sing 1.08 N N
50 C18 H15 C H sing 1.08 N N
51 N4 H16 N H sing 0.97 N N
52 C21 H17 C H sing 1.09 N N
53 C21 H18 C H sing 1.09 N N
54 C22 H19 C H sing 1.09 N N
55 C22 H20 C H sing 1.09 N N
56 C22 H21 C H sing 1.09 N N



XL5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XL5 6nvj Open in New Window Bound ligand 1 1