Chemical Components in the PDB

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RYA : Summary

Code

RYA

One-letter code

X

Molecule name

(7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one

Formula

C17 H15 F2 N5 O2

Formal charge

0

Molecular weight

359.33 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(C)C1=O
SMILES OpenEye OEToolkits 2.0.7 CC1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)C
Canonical SMILES CACTVS 3.385 C[C@H]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(C)C1=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H]1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)C

IUPAC InChI

InChI=1S/C17H15F2N5O2/c1-4-5-24-9(2)16(26)23(3)13-8-20-17(22-15(13)24)21-10-6-11(18)14(25)12(19)7-10/h1,6-9,25H,5H2,2-3H3,(H,20,21,22)/t9-/m1/s1

IUPAC InChI key

DYKLQWQETZOVEI-SECBINFHSA-N
RYA

wwPDB Information

Atom count

41 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-03-02

Last modified at

2020-03-06

Status

Released

Obsoleted

Not Assigned



RYA : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -1.997 -1.028 -0.098
2 C14 C C2 N Y N 0 2.807 -0.652 0.569
3 C5 C C3 N Y N 0 0.174 0.468 0.353
4 C6 C C4 N Y N 0 -0.741 -1.503 -0.423
5 C9 C C8 N Y N 0 2.576 0.7 0.353
6 C11 C C5 N Y N 0 4.863 0.986 -0.319
7 C7 C C6 N N N 0 -3.059 -3.24 -0.548
8 C8 C C7 N N N 0 -3.321 2.212 0.928
9 C10 C C9 N Y N 0 3.606 1.518 -0.092
10 C12 C C10 N Y N 0 5.093 -0.367 -0.108
11 C13 C C11 N Y N 0 4.064 -1.184 0.342
12 N1 N N1 N N N 0 -3.359 0.749 0.805
13 N2 N N2 N N N 0 -3.149 -1.795 -0.328
14 C3 C C12 N Y N 0 -2.115 0.247 0.468
15 N3 N N3 N Y N 0 -1.014 0.96 0.675
16 C1 C C13 N N N 0 -4.346 -1.165 -0.342
17 C2 C C14 R N N 0 -4.398 0.328 -0.141
18 N4 N N4 N Y N 0 0.314 -0.733 -0.186
19 O1 O O1 N N N 0 -5.368 -1.795 -0.514
20 N5 N N5 N N N 0 1.304 1.238 0.582
21 O2 O O2 N N N 0 6.329 -0.89 -0.331
22 F1 F F1 N N N 0 4.291 -2.498 0.559
23 F2 F F2 N N N 0 5.864 1.78 -0.757
24 H1 H H1 N N N 0 2.007 -1.287 0.919
25 C15 C C15 N N N 0 -2.929 2.803 -0.363
26 C16 C C16 N N N 0 -2.617 3.274 -1.392
27 C17 C C17 N N N 0 -5.772 0.718 0.409
28 H2 H H2 N N N 0 -0.62 -2.482 -0.863
29 H3 H H3 N N N 0 -3.132 -3.759 0.408
30 H4 H H4 N N N 0 -3.872 -3.561 -1.198
31 H5 H H5 N N N 0 -2.104 -3.477 -1.018
32 H6 H H6 N N N 0 -4.308 2.579 1.21
33 H7 H H7 N N N 0 -2.596 2.494 1.691
34 H8 H H8 N N N 0 3.427 2.569 -0.26
35 H9 H H9 N N N 0 -4.239 0.826 -1.097
36 H10 H H10 N N N 0 1.214 2.15 0.901
37 H11 H H11 N N N 0 6.909 -0.873 0.442
38 H12 H H12 N N N 0 -2.337 3.695 -2.312
39 H13 H H13 N N N 0 -5.816 1.799 0.542
40 H14 H H14 N N N 0 -6.545 0.406 -0.292
41 H15 H H15 N N N 0 -5.932 0.227 1.369



RYA : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F2 C11 F C sing 1.35 N N
2 N4 C6 N C doub 1.33 N Y
3 N4 C5 N C sing 1.32 N Y
4 C10 C11 C C doub 1.38 N Y
5 C10 C9 C C sing 1.39 N Y
6 N5 C5 N C sing 1.39 N N
7 N5 C9 N C sing 1.4 N N
8 C6 C4 C C sing 1.38 N Y
9 C11 C12 C C sing 1.39 N Y
10 C5 N3 C N doub 1.33 N Y
11 C9 C14 C C doub 1.39 N Y
12 C7 N2 C N sing 1.46 N N
13 C4 N2 C N sing 1.4 N N
14 C4 C3 C C doub 1.4 N Y
15 C12 O2 C O sing 1.36 N N
16 C12 C13 C C doub 1.39 N Y
17 N3 C3 N C sing 1.33 N Y
18 C14 C13 C C sing 1.38 N Y
19 N2 C1 N C sing 1.35 N N
20 C3 N1 C N sing 1.38 N N
21 C13 F1 C F sing 1.35 N N
22 C1 O1 C O doub 1.21 N N
23 C1 C2 C C sing 1.51 N N
24 N1 C2 N C sing 1.47 N N
25 N1 C8 N C sing 1.47 N N
26 C2 C17 C C sing 1.53 N N
27 C8 C15 C C sing 1.47 N N
28 C15 C16 C C trip 1.17 N N
29 C14 H1 C H sing 1.08 N N
30 C6 H2 C H sing 1.08 N N
31 C7 H3 C H sing 1.09 N N
32 C7 H4 C H sing 1.09 N N
33 C7 H5 C H sing 1.09 N N
34 C8 H6 C H sing 1.09 N N
35 C8 H7 C H sing 1.09 N N
36 C10 H8 C H sing 1.08 N N
37 C2 H9 C H sing 1.09 N N
38 N5 H10 N H sing 0.97 N N
39 O2 H11 O H sing 0.97 N N
40 C16 H12 C H sing 1.05 N N
41 C17 H13 C H sing 1.09 N N
42 C17 H14 C H sing 1.09 N N
43 C17 H15 C H sing 1.09 N N



RYA : Used in PDB Entries

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