Chemical Components in the PDB

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13V : Summary

Code

13V

One-letter code

X

Molecule name

4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol

Systematic names

ProgramVersionName
ACDLabs 12.01 4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol
OpenEye OEToolkits 1.7.6 4-[3-[2-azanyl-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl]-2-methyl-but-3-yn-2-ol

Formula

C20 H22 N4 O3

Formal charge

0

Molecular weight

366.414 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O(C)CCOc3cnc(nc3c2c1cc(C#CC(O)(C)C)ccc1nc2)N
SMILES CACTVS 3.370 COCCOc1cnc(N)nc1c2c[nH]c3ccc(cc23)C#CC(C)(C)O
SMILES OpenEye OEToolkits 1.7.6 CC(C)(C#Cc1ccc2c(c1)c(c[nH]2)c3c(cnc(n3)N)OCCOC)O
Canonical SMILES CACTVS 3.370 COCCOc1cnc(N)nc1c2c[nH]c3ccc(cc23)C#CC(C)(C)O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)(C#Cc1ccc2c(c1)c(c[nH]2)c3c(cnc(n3)N)OCCOC)O

IUPAC InChI

InChI=1S/C20H22N4O3/c1-20(2,25)7-6-13-4-5-16-14(10-13)15(11-22-16)18-17(27-9-8-26-3)12-23-19(21)24-18/h4-5,10-12,22,25H,8-9H2,1-3H3,(H2,21,23,24)

IUPAC InChI key

ZZIZLABGKZWVAW-UHFFFAOYSA-N
13V

wwPDB Information

Atom count

49 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-11

Last modified at

2013-04-12

Status

Released

Obsoleted

Not Assigned



13V : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N3 N N3 N N N 0 -0.122 4.082 -0.091
2 C15 C C15 N Y N 0 0.875 3.123 -0.0070
3 N2 N N2 N Y N 0 0.536 1.845 0.04
4 N4 N N4 N Y N 0 2.141 3.511 0.018
5 C16 C C16 N Y N 0 3.126 2.627 0.097
6 C17 C C17 N Y N 0 2.82 1.276 0.154
7 O2 O O2 N N N 0 3.805 0.342 0.236
8 C18 C C18 N N N 0 5.152 0.819 0.265
9 C19 C C19 N N N 0 6.112 -0.368 0.358
10 O3 O O3 N N N 0 6.015 -1.154 -0.832
11 C20 C C20 N N N 0 6.875 -2.294 -0.848
12 C14 C C14 N Y N 0 1.469 0.897 0.12
13 C11 C C11 N Y N 0 1.088 -0.531 0.179
14 C10 C C10 N Y N 0 1.93 -1.592 0.273
15 N1 N N1 N Y N 0 1.211 -2.749 0.308
16 C12 C C12 N Y N 0 -0.279 -1.078 0.153
17 C9 C C9 N Y N 0 -0.138 -2.475 0.237
18 C8 C C8 N Y N 0 -1.273 -3.282 0.235
19 C7 C C7 N Y N 0 -2.515 -2.721 0.152
20 C13 C C13 N Y N 0 -1.546 -0.508 0.073
21 C6 C C6 N Y N 0 -2.666 -1.332 0.068
22 C5 C C5 N N N 0 -3.976 -0.759 -0.018
23 C4 C C4 N N N 0 -5.049 -0.289 -0.089
24 C1 C C1 N N N 0 -6.395 0.3 -0.178
25 C3 C C3 N N N 0 -6.281 1.824 -0.258
26 C2 C C2 N N N 0 -7.1 -0.225 -1.43
27 O1 O O1 N N N 0 -7.151 -0.06 0.98
28 H1 H H1 N N N 0 -1.054 3.813 -0.115
29 H2 H H2 N N N 0 0.111 5.023 -0.123
30 H3 H H3 N N N 0 4.154 2.955 0.116
31 H4 H H4 N N N 0 5.357 1.382 -0.645
32 H5 H H5 N N N 0 5.289 1.466 1.131
33 H6 H H6 N N N 0 7.132 -0.0030 0.469
34 H7 H H7 N N N 0 5.849 -0.982 1.22
35 H8 H H8 N N N 0 7.912 -1.968 -0.761
36 H9 H H9 N N N 0 6.629 -2.947 -0.011
37 H10 H H10 N N N 0 6.742 -2.837 -1.784
38 H11 H H11 N N N 0 3.007 -1.529 0.313
39 H12 H H12 N N N 0 1.594 -3.638 0.373
40 H13 H H13 N N N 0 -1.17 -4.355 0.299
41 H14 H H14 N N N 0 -3.389 -3.356 0.151
42 H15 H H15 N N N 0 -1.657 0.564 0.013
43 H16 H H16 N N N 0 -5.705 2.099 -1.142
44 H17 H H17 N N N 0 -7.277 2.26 -0.324
45 H18 H H18 N N N 0 -5.779 2.198 0.634
46 H19 H H19 N N N 0 -7.182 -1.31 -1.373
47 H20 H H20 N N N 0 -8.097 0.212 -1.496
48 H21 H H21 N N N 0 -6.524 0.05 -2.314
49 H22 H H22 N N N 0 -8.05 0.294 0.989



13V : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 O3 C O sing 1.43 N N
2 O3 C19 O C sing 1.43 N N
3 C19 C18 C C sing 1.53 N N
4 C18 O2 C O sing 1.43 N N
5 N1 C10 N C sing 1.36 N Y
6 N1 C9 N C sing 1.38 N Y
7 C10 C11 C C doub 1.36 N Y
8 C8 C9 C C doub 1.39 N Y
9 C8 C7 C C sing 1.37 N Y
10 C9 C12 C C sing 1.41 N Y
11 O2 C17 O C sing 1.36 N N
12 C11 C12 C C sing 1.47 N Y
13 C11 C14 C C sing 1.48 N N
14 C7 C6 C C doub 1.4 N Y
15 C17 C14 C C doub 1.4 N Y
16 C17 C16 C C sing 1.39 N Y
17 C12 C13 C C doub 1.39 N Y
18 C14 N2 C N sing 1.33 N Y
19 C16 N4 C N doub 1.33 N Y
20 C6 C13 C C sing 1.39 N Y
21 C6 C5 C C sing 1.43 N N
22 N2 C15 N C doub 1.32 N Y
23 N4 C15 N C sing 1.32 N Y
24 C5 C4 C C trip 1.17 N N
25 C15 N3 C N sing 1.39 N N
26 O1 C1 O C sing 1.43 N N
27 C2 C1 C C sing 1.53 N N
28 C4 C1 C C sing 1.47 N N
29 C1 C3 C C sing 1.53 N N
30 N3 H1 N H sing 0.97 N N
31 N3 H2 N H sing 0.97 N N
32 C16 H3 C H sing 1.08 N N
33 C18 H4 C H sing 1.09 N N
34 C18 H5 C H sing 1.09 N N
35 C19 H6 C H sing 1.09 N N
36 C19 H7 C H sing 1.09 N N
37 C20 H8 C H sing 1.09 N N
38 C20 H9 C H sing 1.09 N N
39 C20 H10 C H sing 1.09 N N
40 C10 H11 C H sing 1.08 N N
41 N1 H12 N H sing 0.97 N N
42 C8 H13 C H sing 1.08 N N
43 C7 H14 C H sing 1.08 N N
44 C13 H15 C H sing 1.08 N N
45 C3 H16 C H sing 1.09 N N
46 C3 H17 C H sing 1.09 N N
47 C3 H18 C H sing 1.09 N N
48 C2 H19 C H sing 1.09 N N
49 C2 H20 C H sing 1.09 N N
50 C2 H21 C H sing 1.09 N N
51 O1 H22 O H sing 0.97 N N



13V : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
13V 4idv Open in New Window Bound ligand 4 1