Chemical Components in the PDB

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Y3T : Summary

Code

Y3T

One-letter code

X

Molecule name

N-(3-chloro-4-fluorophenyl)-3-[4-(dimethylamino)butanamido]-4-methoxybenzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(3-chloro-4-fluorophenyl)-3-[4-(dimethylamino)butanamido]-4-methoxybenzamide
OpenEye OEToolkits 2.0.7 ~{N}-(3-chloranyl-4-fluoranyl-phenyl)-3-[4-(dimethylamino)butanoylamino]-4-methoxy-benzamide

Formula

C20 H23 Cl F N3 O3

Formal charge

0

Molecular weight

407.866 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Fc1ccc(NC(=O)c2ccc(OC)c(NC(=O)CCCN(C)C)c2)cc1Cl
SMILES CACTVS 3.385 COc1ccc(cc1NC(=O)CCCN(C)C)C(=O)Nc2ccc(F)c(Cl)c2
SMILES OpenEye OEToolkits 2.0.7 CN(C)CCCC(=O)Nc1cc(ccc1OC)C(=O)Nc2ccc(c(c2)Cl)F
Canonical SMILES CACTVS 3.385 COc1ccc(cc1NC(=O)CCCN(C)C)C(=O)Nc2ccc(F)c(Cl)c2
Canonical SMILES OpenEye OEToolkits 2.0.7 CN(C)CCCC(=O)Nc1cc(ccc1OC)C(=O)Nc2ccc(c(c2)Cl)F

IUPAC InChI

InChI=1S/C20H23ClFN3O3/c1-25(2)10-4-5-19(26)24-17-11-13(6-9-18(17)28-3)20(27)23-14-7-8-16(22)15(21)12-14/h6-9,11-12H,4-5,10H2,1-3H3,(H,23,27)(H,24,26)

IUPAC InChI key

VFCRGORDSAIMRG-UHFFFAOYSA-N
Y3T

wwPDB Information

Atom count

51 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-01-03

Last modified at

2024-02-23

Status

Released

Obsoleted

Not Assigned



Y3T : 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 C02 C C1 N N N 0 1.647 -0.85 0.063
2 C03 C C2 N Y N 0 0.473 -1.743 0.109
3 C04 C C3 N Y N 0 -0.797 -1.217 0.358
4 C05 C C4 N Y N 0 -1.893 -2.058 0.4
5 C06 C C5 N Y N 0 -1.729 -3.429 0.193
6 C07 C C6 N Y N 0 -0.467 -3.949 -0.054
7 C12 C C7 N Y N 0 3.968 -0.5 -0.327
8 C13 C C8 N Y N 0 4.049 0.656 0.44
9 C14 C C9 N Y N 0 5.134 1.5 0.301
10 C15 C C10 N Y N 0 6.141 1.194 -0.601
11 C16 C C11 N Y N 0 6.061 0.043 -1.365
12 C17 C C12 N Y N 0 4.981 -0.807 -1.226
13 C20 C C13 N N N 0 -2.566 -5.646 0.015
14 C21 C C14 N N N 0 -3.501 -0.315 0.183
15 C22 C C15 N N N 0 -4.904 0.205 0.363
16 C24 C C16 N N N 0 -6.437 2.13 -0.07
17 C27 C C17 N N N 0 -7.942 3.913 -0.719
18 O25 O O1 N N N 0 -2.67 0.364 -0.382
19 C08 C C18 N Y N 0 0.629 -3.115 -0.103
20 C23 C C19 N N N 0 -5.013 1.602 -0.253
21 C28 C C20 N N N 0 -5.714 4.436 0.074
22 F18 F F1 N N N 0 7.201 2.021 -0.735
23 N01 N N1 N N N 0 -3.169 -1.535 0.65
24 N11 N N2 N N N 0 2.871 -1.357 -0.188
25 N26 N N3 N N N 0 -6.542 3.47 -0.661
26 O09 O O2 N N N 0 -2.806 -4.254 0.235
27 O10 O O3 N N N 0 1.51 0.344 0.247
28 CL19 CL CL1 N N N 0 5.236 2.945 1.258
29 H1 H H1 N N N 0 -0.922 -0.156 0.518
30 H2 H H2 N N N 0 -0.343 -5.01 -0.213
31 H3 H H3 N N N 0 3.265 0.894 1.143
32 H4 H H4 N N N 0 6.846 -0.193 -2.068
33 H5 H H5 N N N 0 4.919 -1.705 -1.823
34 H6 H H6 N N N 0 -3.508 -6.191 0.075
35 H7 H H7 N N N 0 -2.127 -5.787 -0.972
36 H8 H H8 N N N 0 -1.88 -6.021 0.775
37 H9 H H9 N N N 0 -5.606 -0.466 -0.132
38 H10 H H10 N N N 0 -5.138 0.257 1.426
39 H11 H H11 N N N 0 -7.14 1.459 -0.565
40 H12 H H12 N N N 0 -6.672 2.182 0.993
41 H13 H H13 N N N 0 -8.355 3.942 0.289
42 H14 H H14 N N N 0 -7.99 4.908 -1.161
43 H15 H H15 N N N 0 -8.518 3.216 -1.328
44 H16 H H16 N N N 0 1.61 -3.523 -0.3
45 H17 H H17 N N N 0 -4.31 2.273 0.242
46 H18 H H18 N N N 0 -4.778 1.549 -1.316
47 H19 H H19 N N N 0 -4.672 4.12 0.041
48 H20 H H20 N N N 0 -5.81 5.42 -0.385
49 H21 H H21 N N N 0 -6.047 4.484 1.111
50 H22 H H22 N N N 0 -3.814 -2.051 1.159
51 H23 H H23 N N N 0 2.99 -2.316 -0.273



Y3T : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C24 C23 C C sing 1.53 N N
2 C24 N26 C N sing 1.47 N N
3 C28 N26 C N sing 1.47 N N
4 C23 C22 C C sing 1.53 N N
5 C27 N26 C N sing 1.47 N N
6 C22 C21 C C sing 1.51 N N
7 O25 C21 O C doub 1.21 N N
8 F18 C15 F C sing 1.35 N N
9 C16 C15 C C doub 1.38 N Y
10 C16 C17 C C sing 1.38 N Y
11 C21 N01 C N sing 1.35 N N
12 C15 C14 C C sing 1.39 N Y
13 C17 C12 C C doub 1.39 N Y
14 C14 CL19 C CL sing 1.74 N N
15 C14 C13 C C doub 1.38 N Y
16 C12 C13 C C sing 1.39 N Y
17 C12 N11 C N sing 1.4 N N
18 N11 C02 N C sing 1.35 N N
19 N01 C05 N C sing 1.4 N N
20 C04 C05 C C doub 1.38 N Y
21 C04 C03 C C sing 1.4 N Y
22 C05 C06 C C sing 1.4 N Y
23 C02 C03 C C sing 1.48 N N
24 C02 O10 C O doub 1.22 N N
25 C03 C08 C C doub 1.4 N Y
26 C06 O09 C O sing 1.36 N N
27 C06 C07 C C doub 1.39 N Y
28 O09 C20 O C sing 1.43 N N
29 C08 C07 C C sing 1.38 N Y
30 C04 H1 C H sing 1.08 N N
31 C07 H2 C H sing 1.08 N N
32 C13 H3 C H sing 1.08 N N
33 C16 H4 C H sing 1.08 N N
34 C17 H5 C H sing 1.08 N N
35 C20 H6 C H sing 1.09 N N
36 C20 H7 C H sing 1.09 N N
37 C20 H8 C H sing 1.09 N N
38 C22 H9 C H sing 1.09 N N
39 C22 H10 C H sing 1.09 N N
40 C24 H11 C H sing 1.09 N N
41 C24 H12 C H sing 1.09 N N
42 C27 H13 C H sing 1.09 N N
43 C27 H14 C H sing 1.09 N N
44 C27 H15 C H sing 1.09 N N
45 C08 H16 C H sing 1.08 N N
46 C23 H17 C H sing 1.09 N N
47 C23 H18 C H sing 1.09 N N
48 C28 H19 C H sing 1.09 N N
49 C28 H20 C H sing 1.09 N N
50 C28 H21 C H sing 1.09 N N
51 N01 H22 N H sing 0.97 N N
52 N11 H23 N H sing 0.97 N N



Y3T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Y3T 8fmu Open in New Window Bound ligand 2 1