Chemical Components in the PDB

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2Y9 : Summary

Code

2Y9

One-letter code

X

Molecule name

(3S,4R,5R)-N-cyclopropyl-N'-[(2R)-1-ethoxy-4-methylpentan-2-yl]-4-hydroxy-N-[5-(propan-2-yl)pyridin-2-yl]piperidine-3,5-dicarboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S,4R,5R)-N-cyclopropyl-N'-[(2R)-1-ethoxy-4-methylpentan-2-yl]-4-hydroxy-N-[5-(propan-2-yl)pyridin-2-yl]piperidine-3,5-dicarboxamide
OpenEye OEToolkits 1.7.6 (3S,4R,5R)-N3-cyclopropyl-N5-[(2R)-1-ethoxy-4-methyl-pentan-2-yl]-4-oxidanyl-N3-(5-propan-2-ylpyridin-2-yl)piperidine-3,5-dicarboxamide

Formula

C26 H42 N4 O4

Formal charge

0

Molecular weight

474.636 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N(c1ncc(cc1)C(C)C)C2CC2)C3C(O)C(C(=O)NC(CC(C)C)COCC)CNC3
SMILES CACTVS 3.385 CCOC[CH](CC(C)C)NC(=O)[CH]1CNC[CH]([CH]1O)C(=O)N(C2CC2)c3ccc(cn3)C(C)C
SMILES OpenEye OEToolkits 1.7.6 CCOCC(CC(C)C)NC(=O)C1CNCC(C1O)C(=O)N(c2ccc(cn2)C(C)C)C3CC3
Canonical SMILES CACTVS 3.385 CCOC[C@@H](CC(C)C)NC(=O)[C@@H]1CNC[C@@H]([C@@H]1O)C(=O)N(C2CC2)c3ccc(cn3)C(C)C
Canonical SMILES OpenEye OEToolkits 1.7.6 CCOC[C@@H](CC(C)C)NC(=O)[C@@H]1CNC[C@@H]([C@@H]1O)C(=O)N(c2ccc(cn2)C(C)C)C3CC3

IUPAC InChI

InChI=1S/C26H42N4O4/c1-6-34-15-19(11-16(2)3)29-25(32)21-13-27-14-22(24(21)31)26(33)30(20-8-9-20)23-10-7-18(12-28-23)17(4)5/h7,10,12,16-17,19-22,24,27,31H,6,8-9,11,13-15H2,1-5H3,(H,29,32)/t19-,21-,22+,24-/m1/s1

IUPAC InChI key

YOVGCKBDPOHLAV-CNIHBODFSA-N
2Y9

wwPDB Information

Atom count

76 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-04-11

Last modified at

2014-08-01

Status

Released

Obsoleted

Not Assigned



2Y9 : Atoms of Molecule

Total Number of Atoms: 76
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 1.149 -0.145 -1.156
2 C2 C C2 S N N 0 1.1 -0.734 0.255
3 C3 C C3 R N N 0 -0.329 -1.186 0.566
4 C4 C C4 R N N 0 -1.277 0.008 0.419
5 C5 C C5 N N N 0 -1.159 0.575 -0.998
6 N6 N N6 N N N 0 0.227 0.994 -1.245
7 C7 C C7 N N N 0 2.031 -1.916 0.34
8 C8 C C8 N N N 0 -2.694 -0.441 0.665
9 O9 O O9 N N N 0 -2.925 -1.601 0.931
10 N10 N N10 N N N 0 3.365 -1.727 0.311
11 O11 O O11 N N N 0 1.58 -3.037 0.435
12 N12 N N12 N N N 0 -3.705 0.447 0.589
13 O13 O O13 N N N 0 -0.713 -2.216 -0.347
14 C14 C C14 N N N 0 4.268 -2.88 0.297
15 C15 C C15 N Y N 0 3.885 -0.433 0.295
16 C16 C C16 N N N 0 5.281 -2.97 -0.846
17 C17 C C17 N N N 0 5.752 -2.619 0.566
18 C18 C C18 N Y N 0 3.714 0.392 1.4
19 C19 C C19 N Y N 0 4.236 1.674 1.37
20 C20 C C20 N Y N 0 4.914 2.086 0.232
21 C21 C C21 N Y N 0 5.047 1.213 -0.83
22 N22 N N22 N Y N 0 4.543 -0.005 -0.771
23 C23 C C23 N N N 0 5.499 3.473 0.155
24 C24 C C24 N N N 0 7.012 3.378 -0.051
25 C25 C C25 N N N 0 4.871 4.227 -1.019
26 C26 C C26 R N N 0 -5.083 0.01 0.828
27 C27 C C27 N N N 0 -5.673 -0.55 -0.468
28 C28 C C28 N N N 0 -4.911 -1.815 -0.869
29 C29 C C29 N N N 0 -5.138 -2.903 0.183
30 C30 C C30 N N N 0 -5.417 -2.306 -2.227
31 C31 C C31 N N N 0 -5.922 1.201 1.296
32 O32 O O32 N N N 0 -6.008 2.166 0.245
33 C33 C C33 N N N 0 -6.774 3.324 0.58
34 C34 C C34 N N N 0 -6.798 4.283 -0.612
35 H1 H H1 N N N 0 2.163 0.191 -1.375
36 H2 H H2 N N N 0 0.855 -0.907 -1.878
37 H3 H H3 N N N 0 1.407 0.024 0.976
38 H4 H H4 N N N 0 -0.378 -1.566 1.586
39 H5 H H5 N N N 0 -1.008 0.777 1.143
40 H6 H H6 N N N 0 -1.442 -0.19 -1.72
41 H7 H H7 N N N 0 -1.822 1.435 -1.101
42 H8 H H8 N N N 0 0.31 1.458 -2.137
43 H10 H H10 N N N 0 -3.521 1.375 0.375
44 H11 H H11 N N N 0 -1.61 -2.551 -0.208
45 H12 H H12 N N N 0 3.846 -3.813 0.669
46 H13 H H13 N N N 0 5.525 -3.962 -1.226
47 H14 H H14 N N N 0 5.275 -2.171 -1.588
48 H15 H H15 N N N 0 6.056 -1.589 0.754
49 H16 H H16 N N N 0 6.305 -3.38 1.116
50 H17 H H17 N N N 0 3.18 0.038 2.269
51 H18 H H18 N N N 0 4.118 2.338 2.214
52 H19 H H19 N N N 0 5.574 1.53 -1.718
53 H20 H H20 N N N 0 5.291 4.007 1.082
54 H21 H H21 N N N 0 7.22 2.844 -0.979
55 H22 H H22 N N N 0 7.435 4.381 -0.107
56 H23 H H23 N N N 0 7.459 2.841 0.785
57 H24 H H24 N N N 0 3.793 4.295 -0.873
58 H25 H H25 N N N 0 5.294 5.23 -1.075
59 H26 H H26 N N N 0 5.078 3.693 -1.947
60 H27 H H27 N N N 0 -5.091 -0.764 1.595
61 H28 H H28 N N N 0 -6.724 -0.793 -0.314
62 H29 H H29 N N N 0 -5.584 0.194 -1.26
63 H30 H H30 N N N 0 -3.846 -1.592 -0.937
64 H31 H H31 N N N 0 -4.596 -3.804 -0.103
65 H32 H H32 N N N 0 -4.778 -2.553 1.15
66 H33 H H33 N N N 0 -6.203 -3.126 0.25
67 H34 H H34 N N N 0 -6.481 -2.529 -2.16
68 H35 H H35 N N N 0 -5.255 -1.531 -2.977
69 H36 H H36 N N N 0 -4.874 -3.207 -2.513
70 H37 H H37 N N N 0 -6.923 0.86 1.559
71 H38 H H38 N N N 0 -5.452 1.656 2.168
72 H39 H H39 N N N 0 -7.793 3.027 0.828
73 H40 H H40 N N N 0 -6.322 3.823 1.438
74 H41 H H41 N N N 0 -5.779 4.58 -0.86
75 H42 H H42 N N N 0 -7.25 3.784 -1.47
76 H43 H H43 N N N 0 -7.382 5.167 -0.356



2Y9 : Chemical Bonds

Total Number of Bonds: 78
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C30 C28 C C sing 1.53 N N
2 N6 C5 N C sing 1.47 N N
3 N6 C1 N C sing 1.47 N N
4 C28 C29 C C sing 1.53 N N
5 C28 C27 C C sing 1.53 N N
6 C5 C4 C C sing 1.53 N N
7 C1 C2 C C sing 1.53 N N
8 C27 C26 C C sing 1.53 N N
9 C4 C8 C C sing 1.51 N N
10 C4 C3 C C sing 1.53 N N
11 C2 C3 C C sing 1.53 N N
12 C2 C7 C C sing 1.51 N N
13 O13 C3 O C sing 1.43 N N
14 N12 C8 N C sing 1.35 N N
15 N12 C26 N C sing 1.47 N N
16 C8 O9 C O doub 1.21 N N
17 O11 C7 O C doub 1.21 N N
18 C26 C31 C C sing 1.53 N N
19 C7 N10 C N sing 1.35 N N
20 C31 O32 C O sing 1.43 N N
21 C18 C15 C C doub 1.39 N Y
22 C18 C19 C C sing 1.38 N Y
23 N10 C14 N C sing 1.46 N N
24 N10 C15 N C sing 1.39 N N
25 C14 C16 C C sing 1.53 N N
26 C14 C17 C C sing 1.53 N N
27 O32 C33 O C sing 1.43 N N
28 C15 N22 C N sing 1.32 N Y
29 C19 C20 C C doub 1.39 N Y
30 C16 C17 C C sing 1.53 N N
31 C33 C34 C C sing 1.53 N N
32 N22 C21 N C doub 1.32 N Y
33 C20 C21 C C sing 1.38 N Y
34 C20 C23 C C sing 1.51 N N
35 C25 C23 C C sing 1.53 N N
36 C23 C24 C C sing 1.53 N N
37 C1 H1 C H sing 1.09 N N
38 C1 H2 C H sing 1.09 N N
39 C2 H3 C H sing 1.09 N N
40 C3 H4 C H sing 1.09 N N
41 C4 H5 C H sing 1.09 N N
42 C5 H6 C H sing 1.09 N N
43 C5 H7 C H sing 1.09 N N
44 N6 H8 N H sing 1.01 N N
45 N12 H10 N H sing 0.97 N N
46 O13 H11 O H sing 0.97 N N
47 C14 H12 C H sing 1.09 N N
48 C16 H13 C H sing 1.09 N N
49 C16 H14 C H sing 1.09 N N
50 C17 H15 C H sing 1.09 N N
51 C17 H16 C H sing 1.09 N N
52 C18 H17 C H sing 1.08 N N
53 C19 H18 C H sing 1.08 N N
54 C21 H19 C H sing 1.08 N N
55 C23 H20 C H sing 1.09 N N
56 C24 H21 C H sing 1.09 N N
57 C24 H22 C H sing 1.09 N N
58 C24 H23 C H sing 1.09 N N
59 C25 H24 C H sing 1.09 N N
60 C25 H25 C H sing 1.09 N N
61 C25 H26 C H sing 1.09 N N
62 C26 H27 C H sing 1.09 N N
63 C27 H28 C H sing 1.09 N N
64 C27 H29 C H sing 1.09 N N
65 C28 H30 C H sing 1.09 N N
66 C29 H31 C H sing 1.09 N N
67 C29 H32 C H sing 1.09 N N
68 C29 H33 C H sing 1.09 N N
69 C30 H34 C H sing 1.09 N N
70 C30 H35 C H sing 1.09 N N
71 C30 H36 C H sing 1.09 N N
72 C31 H37 C H sing 1.09 N N
73 C31 H38 C H sing 1.09 N N
74 C33 H39 C H sing 1.09 N N
75 C33 H40 C H sing 1.09 N N
76 C34 H41 C H sing 1.09 N N
77 C34 H42 C H sing 1.09 N N
78 C34 H43 C H sing 1.09 N N



2Y9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2Y9 4q1n Open in New Window Bound ligand 2 1