Chemical Components in the PDB

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C5I : Summary

Code

C5I

One-letter code

X

Molecule name

3-oxo-3-[(3R)-3-(pyrrolo[2,3-b][1,2,3]triazolo[4,5-d]pyridin-1(6H)-yl)piperidin-1-yl]propanenitrile

Systematic names

ProgramVersionName
ACDLabs 12.01 3-oxo-3-[(3R)-3-(pyrrolo[2,3-b][1,2,3]triazolo[4,5-d]pyridin-1(6H)-yl)piperidin-1-yl]propanenitrile

Formula

C15 H15 N7 O

Formal charge

0

Molecular weight

309.326 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N#CCC(=O)N4CCCC(n3nnc2cnc1nccc1c23)C4
SMILES CACTVS 3.370 O=C(CC#N)N1CCC[CH](C1)n2nnc3cnc4[nH]ccc4c23
SMILES OpenEye OEToolkits 1.7.6 c1c[nH]c2c1c3c(cn2)nnn3C4CCCN(C4)C(=O)CC#N
Canonical SMILES CACTVS 3.370 O=C(CC#N)N1CCC[C@H](C1)n2nnc3cnc4[nH]ccc4c23
Canonical SMILES OpenEye OEToolkits 1.7.6 c1c[nH]c2c1c3c(cn2)nnn3[C@@H]4CCCN(C4)C(=O)CC#N

IUPAC InChI

InChI=1S/C15H15N7O/c16-5-3-13(23)21-7-1-2-10(9-21)22-14-11-4-6-17-15(11)18-8-12(14)19-20-22/h4,6,8,10H,1-3,7,9H2,(H,17,18)/t10-/m1/s1

IUPAC InChI key

COGIAVJREKAVDL-SNVBAGLBSA-N
C5I

wwPDB Information

Atom count

38 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-12-10

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



C5I : Atoms of Molecule

Total Number of Atoms: 38
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 1.727 -1.962 -0.952
2 C14 C C14 R N N 0 -0.237 0.869 -0.462
3 C16 C C16 N N N 0 -0.565 1.856 -1.585
4 C17 C C17 N N N 0 -1.914 1.49 -2.21
5 C18 C C18 N N N 0 -3.009 1.589 -1.143
6 C2 C C2 N Y N 0 2.564 -3.004 -1.093
7 C20 C C20 N N N 0 -1.313 0.961 0.624
8 C21 C C21 N N N 0 -3.471 -0.186 0.479
9 C23 C C23 N N N 0 -4.818 -0.387 -0.168
10 C24 C C24 N N N 0 -5.542 -1.462 0.53
11 C5 C C5 N Y N 0 3.761 -1.418 -0.043
12 C6 C C6 N Y N 0 2.474 -0.907 -0.269
13 C7 C C7 N Y N 0 2.171 0.395 0.158
14 C8 C C8 N Y N 0 3.177 1.138 0.801
15 C9 C C9 N Y N 0 4.436 0.546 0.985
16 H1 H H1 N N N 0 0.701 -1.913 -1.283
17 H14 H H14 N N N 0 -0.21 -0.144 -0.864
18 H16 H H16 N N N 0 -0.616 2.866 -1.178
19 H16A H H16A N N N 0 0.212 1.811 -2.347
20 H17 H H17 N N N 0 -2.136 2.179 -3.024
21 H17A H H17A N N N 0 -1.872 0.472 -2.595
22 H18 H H18 N N N 0 -3.114 2.625 -0.822
23 H18A H H18A N N N 0 -3.954 1.234 -1.556
24 H2 H H2 N N N 0 2.313 -3.944 -1.561
25 H20 H H20 N N N 0 -1.139 0.192 1.377
26 H20A H H20A N N N 0 -1.28 1.946 1.089
27 H23 H H23 N N N 0 -5.392 0.538 -0.106
28 H23A H H23A N N N 0 -4.681 -0.66 -1.214
29 H9 H H9 N N N 0 5.218 1.105 1.477
30 HN3 H HN3 N N N 0 4.55 -3.287 -0.537
31 N10 N N10 N Y N 0 4.68 -0.674 0.571
32 N11 N N11 N Y N 0 2.657 2.34 1.115
33 N12 N N12 N Y N 0 1.431 2.41 0.729
34 N13 N N13 N Y N 0 1.069 1.201 0.114
35 N19 N N19 N N N 0 -2.629 0.753 0.0040
36 N25 N N25 N N N 0 -6.1 -2.292 1.068
37 N3 N N3 N Y N 0 3.783 -2.694 -0.555
38 O22 O O22 N N N 0 -3.146 -0.869 1.426



C5I : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.34 N Y
2 C1 C6 C C sing 1.46 N Y
3 C2 N3 C N sing 1.37 N Y
4 N3 C5 N C sing 1.38 N Y
5 C5 C6 C C doub 1.4 N Y
6 C5 N10 C N sing 1.33 N Y
7 C6 C7 C C sing 1.4 N Y
8 C7 C8 C C doub 1.41 N Y
9 C7 N13 C N sing 1.37 N Y
10 C8 C9 C C sing 1.4 N Y
11 C8 N11 C N sing 1.35 N Y
12 C9 N10 C N doub 1.31 N Y
13 N11 N12 N N doub 1.29 N Y
14 N12 N13 N N sing 1.4 N Y
15 N13 C14 N C sing 1.47 N N
16 C14 C16 C C sing 1.53 N N
17 C14 C20 C C sing 1.53 N N
18 C16 C17 C C sing 1.53 N N
19 C17 C18 C C sing 1.53 N N
20 C18 N19 C N sing 1.47 N N
21 N19 C20 N C sing 1.47 N N
22 N19 C21 N C sing 1.35 N N
23 C21 O22 C O doub 1.21 N N
24 C21 C23 C C sing 1.51 N N
25 C23 C24 C C sing 1.47 N N
26 C24 N25 C N trip 1.14 N N
27 C1 H1 C H sing 1.08 N N
28 C2 H2 C H sing 1.08 N N
29 N3 HN3 N H sing 0.97 N N
30 C9 H9 C H sing 1.08 N N
31 C14 H14 C H sing 1.09 N N
32 C16 H16 C H sing 1.09 N N
33 C16 H16A C H sing 1.09 N N
34 C17 H17 C H sing 1.09 N N
35 C17 H17A C H sing 1.09 N N
36 C18 H18 C H sing 1.09 N N
37 C18 H18A C H sing 1.09 N N
38 C20 H20 C H sing 1.09 N N
39 C20 H20A C H sing 1.09 N N
40 C23 H23 C H sing 1.09 N N
41 C23 H23A C H sing 1.09 N N



C5I : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
C5I 4i5c Open in New Window Bound ligand 2 1