Chemical Components in the PDB

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R5D : Summary

Code

R5D

One-letter code

X

Molecule name

(1R,2R)-2-cyano-N-[(1S,5R)-3-(5-fluoro-2-{[1-(2-hydroxyethyl)-1H-pyrazol-4-yl]amino}pyrimidin-4-yl)-3-azabicyclo[3.1.0]hexan-1-yl]cyclopropane-1-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2R)-2-cyano-N-[(1S,5R)-3-(5-fluoro-2-{[1-(2-hydroxyethyl)-1H-pyrazol-4-yl]amino}pyrimidin-4-yl)-3-azabicyclo[3.1.0]hexan-1-yl]cyclopropane-1-carboxamide
OpenEye OEToolkits 2.0.7 (1~{R},2~{R})-2-cyano-~{N}-[(1~{S},5~{R})-3-[5-fluoranyl-2-[[1-(2-hydroxyethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-1-yl]cyclopropane-1-carboxamide

Formula

C19 H21 F N8 O2

Formal charge

0

Molecular weight

412.421 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N(c1cnn(CCO)c1)c2nc(c(cn2)F)N4CC3C(C3)(C4)NC(C5C(C5)C#N)=O
SMILES CACTVS 3.385 OCCn1cc(Nc2ncc(F)c(n2)N3C[CH]4C[C]4(C3)NC(=O)[CH]5C[CH]5C#N)cn1
SMILES OpenEye OEToolkits 2.0.7 c1c(cn(n1)CCO)Nc2ncc(c(n2)N3CC4CC4(C3)NC(=O)C5CC5C#N)F
Canonical SMILES CACTVS 3.385 OCCn1cc(Nc2ncc(F)c(n2)N3C[C@H]4C[C@]4(C3)NC(=O)[C@@H]5C[C@H]5C#N)cn1
Canonical SMILES OpenEye OEToolkits 2.0.7 c1c(cn(n1)CCO)Nc2ncc(c(n2)N3C[C@H]4C[C@]4(C3)NC(=O)[C@@H]5C[C@H]5C#N)F

IUPAC InChI

InChI=1S/C19H21FN8O2/c20-15-7-22-18(24-13-6-23-28(9-13)1-2-29)25-16(15)27-8-12-4-19(12,10-27)26-17(30)14-3-11(14)5-21/h6-7,9,11-12,14,29H,1-4,8,10H2,(H,26,30)(H,22,24,25)/t11-,12+,14+,19+/m0/s1

IUPAC InChI key

OCNRQCROIYCWQL-QULAYQROSA-N
R5D

wwPDB Information

Atom count

51 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-01-30

Last modified at

2020-04-03

Status

Released

Obsoleted

Not Assigned



R5D : 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 N3 N N1 N N N 0 -2.451 0.567 -0.023
2 C4 C C1 N N N 0 -7.014 2.424 0.088
3 N2 N N2 N Y N 0 -5.926 0.177 0.628
4 C7 C C2 N Y N 0 -1.982 -2.818 0.986
5 C6 C C3 N Y N 0 -1.822 -0.633 0.265
6 C9 C C4 N Y N 0 0.119 -1.873 0.354
7 C13 C C5 S N N 0 3.391 -1.156 -1.034
8 C8 C C6 N Y N 0 -0.618 -2.966 0.82
9 N5 N N3 N Y N 0 -0.512 -0.732 0.097
10 C18 C C7 R N N 0 6.005 2.842 0.549
11 C16 C C8 R N N 0 5.971 1.33 0.314
12 C19 C C9 N N N 0 7.284 3.536 0.33
13 C1 C C10 N Y N 0 -4.713 -0.312 0.597
14 C2 C C11 N Y N 0 -3.842 0.692 0.149
15 C3 C C12 N Y N 0 -4.58 1.807 -0.089
16 N1 N N4 N Y N 0 -5.875 1.511 0.201
17 C5 C C13 N N N 0 -8.087 1.793 -0.802
18 O1 O O1 N N N 0 -9.199 2.684 -0.913
19 N4 N N5 N Y N 0 -2.547 -1.653 0.701
20 N6 N N6 N N N 0 1.491 -1.973 0.177
21 C10 C C14 N N N 0 1.824 -3.026 -0.817
22 C11 C C15 R N N 0 3.246 -2.668 -1.301
23 C12 C C16 N N N 0 3.385 -1.689 -2.468
24 C14 C C17 N N N 0 2.045 -0.727 -0.412
25 N7 N N7 N N N 0 4.622 -0.584 -0.482
26 C15 C C18 N N N 0 4.706 0.742 -0.254
27 O2 O O2 N N N 0 3.763 1.462 -0.507
28 C17 C C19 N N N 0 5.915 1.884 1.739
29 N8 N N8 N N N 0 8.272 4.071 0.161
30 F1 F F1 N N N 0 -0.011 -4.139 1.102
31 H11 H H1 N N N 0 -1.931 1.323 -0.338
32 H7 H H2 N N N 0 -7.429 2.613 1.078
33 H6 H H3 N N N 0 -6.684 3.365 -0.353
34 H12 H H4 N N N 0 -2.582 -3.643 1.34
35 H3 H H5 N N N 0 5.111 3.411 0.293
36 H2 H H6 N N N 0 6.897 0.85 -0.003
37 H4 H H7 N N N 0 -4.43 -1.318 0.87
38 H5 H H8 N N N 0 -4.207 2.756 -0.443
39 H8 H H9 N N N 0 -7.672 1.605 -1.793
40 H9 H H10 N N N 0 -8.417 0.853 -0.362
41 H10 H H11 N N N 0 -9.918 2.348 -1.464
42 H14 H H12 N N N 0 1.82 -4.009 -0.345
43 H13 H H13 N N N 0 1.12 -3.0 -1.648
44 H1 H H14 N N N 0 4.048 -3.37 -1.075
45 H16 H H15 N N N 0 2.498 -1.498 -3.072
46 H15 H H16 N N N 0 4.331 -1.684 -3.01
47 H17 H H17 N N N 0 2.206 0.021 0.365
48 H18 H H18 N N N 0 1.376 -0.34 -1.181
49 H19 H H19 N N N 0 5.376 -1.16 -0.279
50 H20 H H20 N N N 0 6.804 1.768 2.36
51 H21 H H21 N N N 0 4.963 1.823 2.266



R5D : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N8 C19 N C trip 1.14 N N
2 C19 C18 C C sing 1.47 N N
3 C18 C16 C C sing 1.53 N N
4 C18 C17 C C sing 1.53 N N
5 C16 C17 C C sing 1.53 N N
6 C16 C15 C C sing 1.51 N N
7 F1 C8 F C sing 1.35 N N
8 N7 C15 N C sing 1.35 N N
9 N7 C13 N C sing 1.47 N N
10 C15 O2 C O doub 1.21 N N
11 C14 C13 C C sing 1.54 N N
12 C14 N6 C N sing 1.49 N N
13 C8 C7 C C doub 1.38 N Y
14 C8 C9 C C sing 1.4 N Y
15 C7 N4 C N sing 1.33 N Y
16 C13 C12 C C sing 1.53 N N
17 C13 C11 C C sing 1.54 N N
18 N6 C9 N C sing 1.39 N N
19 N6 C10 N C sing 1.49 N N
20 C9 N5 C N doub 1.33 N Y
21 C12 C11 C C sing 1.53 N N
22 N4 C6 N C doub 1.33 N Y
23 C11 C10 C C sing 1.54 N N
24 N5 C6 N C sing 1.32 N Y
25 C6 N3 C N sing 1.39 N N
26 N3 C2 N C sing 1.41 N N
27 C2 C3 C C doub 1.36 N Y
28 C2 C1 C C sing 1.4 N Y
29 C3 N1 C N sing 1.36 N Y
30 C1 N2 C N doub 1.31 N Y
31 N1 N2 N N sing 1.4 N Y
32 N1 C4 N C sing 1.46 N N
33 C4 C5 C C sing 1.53 N N
34 O1 C5 O C sing 1.43 N N
35 N3 H11 N H sing 0.97 N N
36 C4 H7 C H sing 1.09 N N
37 C4 H6 C H sing 1.09 N N
38 C7 H12 C H sing 1.08 N N
39 C18 H3 C H sing 1.09 N N
40 C16 H2 C H sing 1.09 N N
41 C1 H4 C H sing 1.08 N N
42 C3 H5 C H sing 1.08 N N
43 C5 H8 C H sing 1.09 N N
44 C5 H9 C H sing 1.09 N N
45 O1 H10 O H sing 0.97 N N
46 C10 H14 C H sing 1.09 N N
47 C10 H13 C H sing 1.09 N N
48 C11 H1 C H sing 1.09 N N
49 C12 H16 C H sing 1.09 N N
50 C12 H15 C H sing 1.09 N N
51 C14 H17 C H sing 1.09 N N
52 C14 H18 C H sing 1.09 N N
53 N7 H19 N H sing 0.97 N N
54 C17 H20 C H sing 1.09 N N
55 C17 H21 C H sing 1.09 N N



R5D : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
R5D 6vns Open in New Window Bound ligand 1 1