Chemical Components in the PDB

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IA3 : Summary

Code

IA3

One-letter code

X

Molecule name

methyl (Z)-4-(4-(4-chlorobenzyl)-1-(2-fluorobenzyl)piperidin-4-yl)-2-hydroxy-4-oxobut-2-enoate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 methyl (~{Z})-4-[4-[(4-chlorophenyl)methyl]-1-[(2-fluorophenyl)methyl]piperidin-4-yl]-2-oxidanyl-4-oxidanylidene-but-2-enoate

Formula

C24 H25 Cl F N O4

Formal charge

0

Molecular weight

445.911 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COC(=O)C(O)=CC(=O)C1(CCN(CC1)Cc2ccccc2F)Cc3ccc(Cl)cc3
SMILES OpenEye OEToolkits 2.0.7 COC(=O)C(=CC(=O)C1(CCN(CC1)Cc2ccccc2F)Cc3ccc(cc3)Cl)O
Canonical SMILES CACTVS 3.385 COC(=O)\C(O)=C\C(=O)C1(CCN(CC1)Cc2ccccc2F)Cc3ccc(Cl)cc3
Canonical SMILES OpenEye OEToolkits 2.0.7 COC(=O)/C(=C/C(=O)C1(CCN(CC1)Cc2ccccc2F)Cc3ccc(cc3)Cl)/O

IUPAC InChI

InChI=1S/C24H25ClFNO4/c1-31-23(30)21(28)14-22(29)24(15-17-6-8-19(25)9-7-17)10-12-27(13-11-24)16-18-4-2-3-5-20(18)26/h2-9,14,28H,10-13,15-16H2,1H3/b21-14-

IUPAC InChI key

OJDSGFRNRSWSOM-STZFKDTASA-N
IA3

wwPDB Information

Atom count

56 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-06-01

Last modified at

2022-02-11

Status

Released

Obsoleted

Not Assigned



IA3 : Atoms of Molecule

Total Number of Atoms: 56
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -2.085 6.488 -0.005
2 C3 C C2 N N N 0 -1.507 4.18 0.19
3 C5 C C3 N N N 0 -1.496 2.778 -0.292
4 C7 C C4 N N N 0 -0.887 1.814 0.441
5 C8 C C5 N N N 0 -0.711 0.518 -0.101
6 C10 C C6 N N N 0 -0.15 -0.587 0.756
7 C11 C C7 N N N 0 -1.164 -0.958 1.84
8 C12 C C8 N Y N 0 -2.435 -1.446 1.193
9 C13 C C9 N Y N 0 -2.643 -2.801 1.014
10 C14 C C10 N Y N 0 -3.808 -3.249 0.421
11 C15 C C11 N Y N 0 -4.766 -2.341 0.006
12 C17 C C12 N Y N 0 -4.557 -0.985 0.185
13 C18 C C13 N Y N 0 -3.394 -0.538 0.784
14 C19 C C14 N N N 0 0.14 -1.813 -0.115
15 C20 C C15 N N N 0 1.199 -1.451 -1.159
16 C22 C C16 N N N 0 3.508 -0.785 -1.449
17 C23 C C17 N Y N 0 4.797 -0.534 -0.709
18 C24 C C18 N Y N 0 5.464 -1.586 -0.103
19 C26 C C19 N Y N 0 6.648 -1.354 0.576
20 C27 C C20 N Y N 0 7.163 -0.074 0.648
21 C28 C C21 N Y N 0 6.497 0.975 0.043
22 C29 C C22 N Y N 0 5.317 0.744 -0.641
23 C30 C C23 N N N 0 2.181 0.196 0.322
24 C31 C C24 N N N 0 1.152 -0.116 1.411
25 F25 F F1 N N N 0 4.959 -2.837 -0.174
26 N21 N N1 N N N 0 2.425 -1.008 -0.482
27 O2 O O1 N N N 0 -2.112 5.138 -0.539
28 O4 O O2 N N N 0 -0.972 4.464 1.242
29 O6 O O3 N N N 0 -2.092 2.462 -1.464
30 O9 O O4 N N N 0 -1.011 0.297 -1.256
31 CL1 CL CL1 N N N 0 -6.23 -2.902 -0.74
32 H1 H H1 N N N 0 -1.05 6.814 0.106
33 H2 H H2 N N N 0 -2.605 7.159 -0.687
34 H3 H H3 N N N 0 -2.577 6.505 0.967
35 H4 H H4 N N N 0 -0.536 2.035 1.438
36 H5 H H5 N N N 0 -0.751 -1.747 2.469
37 H6 H H6 N N N 0 -1.38 -0.082 2.451
38 H7 H H7 N N N 0 -1.895 -3.509 1.338
39 H8 H H8 N N N 0 -3.971 -4.307 0.281
40 H9 H H9 N N N 0 -5.306 -0.276 -0.135
41 H10 H H10 N N N 0 -3.23 0.52 0.923
42 H11 H H11 N N N 0 0.51 -2.625 0.512
43 H12 H H12 N N N 0 -0.774 -2.127 -0.617
44 H13 H H13 N N N 0 1.418 -2.326 -1.771
45 H14 H H14 N N N 0 0.824 -0.649 -1.794
46 H15 H H15 N N N 0 3.27 0.08 -2.068
47 H16 H H16 N N N 0 3.618 -1.665 -2.082
48 H17 H H17 N N N 0 7.168 -2.174 1.049
49 H18 H H18 N N N 0 8.087 0.107 1.178
50 H19 H H19 N N N 0 6.9 1.975 0.101
51 H20 H H20 N N N 0 4.8 1.564 -1.117
52 H21 H H21 N N N 0 1.801 0.991 -0.319
53 H22 H H22 N N N 0 3.114 0.518 0.786
54 H23 H H23 N N N 0 0.96 0.782 1.998
55 H24 H H24 N N N 0 1.537 -0.902 2.061
56 H26 H H26 N N N 0 -2.121 1.513 -1.646



IA3 : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C5 O C sing 1.35 N N
2 C1 O2 C O sing 1.45 N N
3 O2 C3 O C sing 1.35 N N
4 C5 C3 C C sing 1.48 N N
5 C5 C7 C C doub 1.36 Z N
6 O9 C8 O C doub 1.21 N N
7 C17 C18 C C doub 1.38 N Y
8 C17 C15 C C sing 1.38 N Y
9 C3 O4 C O doub 1.21 N N
10 C18 C12 C C sing 1.38 N Y
11 C8 C7 C C sing 1.42 N N
12 C8 C10 C C sing 1.51 N N
13 CL1 C15 CL C sing 1.74 N N
14 C15 C14 C C doub 1.38 N Y
15 C12 C11 C C sing 1.51 N N
16 C12 C13 C C doub 1.38 N Y
17 C11 C10 C C sing 1.53 N N
18 C10 C19 C C sing 1.53 N N
19 C10 C31 C C sing 1.53 N N
20 C19 C20 C C sing 1.53 N N
21 C20 N21 C N sing 1.47 N N
22 C14 C13 C C sing 1.38 N Y
23 C31 C30 C C sing 1.53 N N
24 N21 C30 N C sing 1.47 N N
25 N21 C22 N C sing 1.47 N N
26 C22 C23 C C sing 1.51 N N
27 C23 C29 C C doub 1.38 N Y
28 C23 C24 C C sing 1.39 N Y
29 C29 C28 C C sing 1.38 N Y
30 F25 C24 F C sing 1.35 N N
31 C24 C26 C C doub 1.38 N Y
32 C28 C27 C C doub 1.38 N Y
33 C26 C27 C C sing 1.38 N Y
34 C1 H1 C H sing 1.09 N N
35 C1 H2 C H sing 1.09 N N
36 C1 H3 C H sing 1.09 N N
37 C7 H4 C H sing 1.08 N N
38 C11 H5 C H sing 1.09 N N
39 C11 H6 C H sing 1.09 N N
40 C13 H7 C H sing 1.08 N N
41 C14 H8 C H sing 1.08 N N
42 C17 H9 C H sing 1.08 N N
43 C18 H10 C H sing 1.08 N N
44 C19 H11 C H sing 1.09 N N
45 C19 H12 C H sing 1.09 N N
46 C20 H13 C H sing 1.09 N N
47 C20 H14 C H sing 1.09 N N
48 C22 H15 C H sing 1.09 N N
49 C22 H16 C H sing 1.09 N N
50 C26 H17 C H sing 1.08 N N
51 C27 H18 C H sing 1.08 N N
52 C28 H19 C H sing 1.08 N N
53 C29 H20 C H sing 1.08 N N
54 C30 H21 C H sing 1.09 N N
55 C30 H22 C H sing 1.09 N N
56 C31 H23 C H sing 1.09 N N
57 C31 H24 C H sing 1.09 N N
58 O6 H26 O H sing 0.97 N N



IA3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IA3 7ex3 Open in New Window Bound ligand 1 1