Chemical Components in the PDB

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NRK : Summary

Code

NRK

One-letter code

X

Molecule name

(1~{R},2~{S})-2-[(2,4-dimethylpyrimidin-5-yl)oxymethyl]-~{N}-(5-fluoranylpyridin-2-yl)-2-(3-fluorophenyl)cyclopropane-1-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (1~{R},2~{S})-2-[(2,4-dimethylpyrimidin-5-yl)oxymethyl]-~{N}-(5-fluoranylpyridin-2-yl)-2-(3-fluorophenyl)cyclopropane-1-carboxamide

Formula

C22 H20 F2 N4 O2

Formal charge

0

Molecular weight

410.417 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1ncc(OC[C]2(C[CH]2C(=O)Nc3ccc(F)cn3)c4cccc(F)c4)c(C)n1
SMILES OpenEye OEToolkits 2.0.7 Cc1c(cnc(n1)C)OCC2(CC2C(=O)Nc3ccc(cn3)F)c4cccc(c4)F
Canonical SMILES CACTVS 3.385 Cc1ncc(OC[C@]2(C[C@H]2C(=O)Nc3ccc(F)cn3)c4cccc(F)c4)c(C)n1
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1c(cnc(n1)C)OC[C@]2(C[C@H]2C(=O)Nc3ccc(cn3)F)c4cccc(c4)F

IUPAC InChI

InChI=1S/C22H20F2N4O2/c1-13-19(11-25-14(2)27-13)30-12-22(15-4-3-5-16(23)8-15)9-18(22)21(29)28-20-7-6-17(24)10-26-20/h3-8,10-11,18H,9,12H2,1-2H3,(H,26,28,29)/t18-,22+/m0/s1

IUPAC InChI key

MUGXRYIUWFITCP-PGRDOPGGSA-N
NRK

wwPDB Information

Atom count

50 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-12-11

Last modified at

2020-01-10

Status

Released

Obsoleted

Not Assigned



NRK : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 R N N 0 -0.741 -2.063 0.535
2 C02 C C2 N N N 0 0.075 -1.95 1.824
3 C03 C C3 S N N 0 0.637 -1.398 0.512
4 C04 C C4 N N N 0 0.684 0.122 0.349
5 C05 C C5 N N N 0 -1.947 -1.171 0.395
6 C06 C C6 N Y N 0 1.765 -2.158 -0.136
7 C07 C C7 N Y N 0 2.921 -2.418 0.576
8 C08 C C8 N Y N 0 3.958 -3.116 -0.02
9 C09 C C9 N Y N 0 3.835 -3.553 -1.328
10 C10 C C10 N Y N 0 2.678 -3.292 -2.038
11 C11 C C11 N Y N 0 1.642 -2.599 -1.44
12 O12 O O1 N N N 0 2.046 0.552 0.285
13 C13 C C12 N Y N 0 2.266 1.885 0.139
14 C14 C C13 N Y N 0 3.56 2.391 0.069
15 N15 N N1 N Y N 0 3.732 3.695 -0.074
16 C16 C C14 N Y N 0 2.699 4.51 -0.149
17 N17 N N2 N Y N 0 1.459 4.069 -0.086
18 C18 C C15 N Y N 0 1.203 2.778 0.051
19 O19 O O2 N N N 0 -1.804 0.027 0.27
20 N20 N N3 N N N 0 -3.185 -1.703 0.409
21 C21 C C16 N Y N 0 -4.295 -0.894 0.165
22 C22 C C17 N Y N 0 -5.557 -1.469 0.067
23 C23 C C18 N Y N 0 -6.65 -0.657 -0.175
24 C24 C C19 N Y N 0 -6.442 0.711 -0.311
25 C25 C C20 N Y N 0 -5.159 1.214 -0.201
26 N26 N N4 N Y N 0 -4.137 0.413 0.035
27 C27 C C21 N N N 0 2.943 5.988 -0.31
28 C28 C C22 N N N 0 4.748 1.468 0.154
29 F29 F F1 N N N 0 -7.483 1.54 -0.548
30 F30 F F2 N N N 0 5.089 -3.37 0.674
31 H011 H H1 N N N 0 -0.831 -3.05 0.081
32 H021 H H2 N N N 0 -0.26 -1.23 2.571
33 H022 H H3 N N N 0 0.523 -2.863 2.219
34 H041 H H4 N N N 0 0.171 0.405 -0.57
35 H042 H H5 N N N 0 0.193 0.595 1.199
36 H071 H H6 N N N 0 3.016 -2.076 1.596
37 H091 H H7 N N N 0 4.643 -4.097 -1.794
38 H101 H H8 N N N 0 2.582 -3.632 -3.058
39 H111 H H9 N N N 0 0.736 -2.399 -1.994
40 H181 H H10 N N N 0 0.184 2.424 0.097
41 H201 H H11 N N N 0 -3.304 -2.649 0.588
42 H221 H H12 N N N 0 -5.682 -2.536 0.177
43 H231 H H13 N N N 0 -7.643 -1.075 -0.257
44 H251 H H14 N N N 0 -4.991 2.276 -0.306
45 H271 H H15 N N N 0 2.989 6.235 -1.371
46 H273 H H16 N N N 0 2.13 6.544 0.157
47 H272 H H17 N N N 0 3.886 6.255 0.166
48 H282 H H18 N N N 0 5.021 1.135 -0.848
49 H281 H H19 N N N 0 5.588 1.997 0.603
50 H283 H H20 N N N 0 4.493 0.604 0.767



NRK : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C02 C01 C C sing 1.53 N N
2 C02 C03 C C sing 1.53 N N
3 C01 C05 C C sing 1.51 N N
4 C01 C03 C C sing 1.53 N N
5 O19 C05 O C doub 1.21 N N
6 C05 N20 C N sing 1.35 N N
7 N20 C21 N C sing 1.4 N N
8 C21 N26 C N doub 1.32 N Y
9 C21 C22 C C sing 1.39 N Y
10 N26 C25 N C sing 1.32 N Y
11 C25 C24 C C doub 1.38 N Y
12 C22 C23 C C doub 1.38 N Y
13 C03 C06 C C sing 1.51 N N
14 C03 C04 C C sing 1.53 N N
15 C24 C23 C C sing 1.39 N Y
16 C24 F29 C F sing 1.35 N N
17 C06 C11 C C doub 1.38 N Y
18 C06 C07 C C sing 1.38 N Y
19 C11 C10 C C sing 1.38 N Y
20 C04 O12 C O sing 1.43 N N
21 C07 C08 C C doub 1.38 N Y
22 C10 C09 C C doub 1.38 N Y
23 C08 C09 C C sing 1.38 N Y
24 C08 F30 C F sing 1.35 N N
25 O12 C13 O C sing 1.36 N N
26 C18 C13 C C doub 1.39 N Y
27 C18 N17 C N sing 1.32 N Y
28 C13 C14 C C sing 1.39 N Y
29 N17 C16 N C doub 1.32 N Y
30 C14 C28 C C sing 1.51 N N
31 C14 N15 C N doub 1.32 N Y
32 C16 N15 C N sing 1.32 N Y
33 C16 C27 C C sing 1.51 N N
34 C01 H011 C H sing 1.09 N N
35 C02 H021 C H sing 1.09 N N
36 C02 H022 C H sing 1.09 N N
37 C04 H041 C H sing 1.09 N N
38 C04 H042 C H sing 1.09 N N
39 C07 H071 C H sing 1.08 N N
40 C09 H091 C H sing 1.08 N N
41 C10 H101 C H sing 1.08 N N
42 C11 H111 C H sing 1.08 N N
43 C18 H181 C H sing 1.08 N N
44 N20 H201 N H sing 0.97 N N
45 C22 H221 C H sing 1.08 N N
46 C23 H231 C H sing 1.08 N N
47 C25 H251 C H sing 1.08 N N
48 C27 H271 C H sing 1.09 N N
49 C27 H273 C H sing 1.09 N N
50 C27 H272 C H sing 1.09 N N
51 C28 H282 C H sing 1.09 N N
52 C28 H281 C H sing 1.09 N N
53 C28 H283 C H sing 1.09 N N



NRK : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NRK 6tot Open in New Window Bound ligand 2 1