Chemical Components in the PDB

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Y5D : Summary

Code

Y5D

One-letter code

X

Molecule name

{1-(ethylsulfonyl)-3-[4-(2-{[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]azetidin-3-yl}acetonitrile

Systematic names

ProgramVersionName
ACDLabs 12.01 {1-(ethylsulfonyl)-3-[4-(2-{[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]azetidin-3-yl}acetonitrile
OpenEye OEToolkits 2.0.7 2-[1-ethylsulfonyl-3-[4-[2-[[3-fluoranyl-4-(1-methylpiperidin-4-yl)phenyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]pyrazol-1-yl]azetidin-3-yl]ethanenitrile

Formula

C28 H32 F N9 O2 S

Formal charge

0

Molecular weight

577.676 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c5c(c4c1c(ncc1)nc(Nc3ccc(C2CCN(C)CC2)c(c3)F)n4)cnn5C6(CN(C6)S(CC)(=O)=O)CC#N
SMILES CACTVS 3.385 CC[S](=O)(=O)N1CC(CC#N)(C1)n2cc(cn2)c3nc(Nc4ccc(C5CCN(C)CC5)c(F)c4)nc6[nH]ccc36
SMILES OpenEye OEToolkits 2.0.7 CCS(=O)(=O)N1CC(C1)(CC#N)n2cc(cn2)c3c4cc[nH]c4nc(n3)Nc5ccc(c(c5)F)C6CCN(CC6)C
Canonical SMILES CACTVS 3.385 CC[S](=O)(=O)N1CC(CC#N)(C1)n2cc(cn2)c3nc(Nc4ccc(C5CCN(C)CC5)c(F)c4)nc6[nH]ccc36
Canonical SMILES OpenEye OEToolkits 2.0.7 CCS(=O)(=O)N1CC(C1)(CC#N)n2cc(cn2)c3c4cc[nH]c4nc(n3)Nc5ccc(c(c5)F)C6CCN(CC6)C

IUPAC InChI

InChI=1S/C28H32FN9O2S/c1-3-41(39,40)37-17-28(18-37,9-10-30)38-16-20(15-32-38)25-23-6-11-31-26(23)35-27(34-25)33-21-4-5-22(24(29)14-21)19-7-12-36(2)13-8-19/h4-6,11,14-16,19H,3,7-9,12-13,17-18H2,1-2H3,(H2,31,33,34,35)

IUPAC InChI key

KODVAIZRONHLFN-UHFFFAOYSA-N
Y5D

wwPDB Information

Atom count

73 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-02-04

Last modified at

2022-01-07

Status

Released

Obsoleted

Not Assigned



Y5D : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 -3.076 -0.769 0.809
2 C13 C C2 N Y N 0 -0.088 -2.399 -0.713
3 C15 C C3 N Y N 0 0.688 -4.289 -1.663
4 C17 C C4 N Y N 0 1.32 -2.364 -0.699
5 C21 C C5 N Y N 0 3.288 0.86 0.771
6 C22 C C6 N Y N 0 3.94 0.339 -0.34
7 C24 C C7 N Y N 0 6.047 1.005 0.583
8 C26 C C8 N N N 0 7.935 1.882 -0.768
9 C04 C C9 N N N 0 -5.622 0.955 1.448
10 C05 C C10 N N N 0 -5.541 -0.562 1.197
11 C06 C C11 N N N 0 -5.77 -1.407 2.451
12 C07 C C12 N N N 0 -5.631 -2.833 2.114
13 C11 C C13 N Y N 0 -2.277 -1.302 -0.164
14 C12 C C14 N Y N 0 -0.797 -1.313 -0.173
15 C14 C C15 N Y N 0 -0.458 -3.663 -1.347
16 C19 C C16 N Y N 0 1.221 -0.3 0.326
17 C23 C C17 N Y N 0 5.316 0.414 -0.431
18 C25 C C18 N N N 0 7.548 1.084 0.481
19 C27 C C19 N N N 0 9.459 1.907 -0.9
20 C29 C C20 N N N 0 9.448 -0.135 -2.201
21 C30 C C21 N N N 0 9.648 -0.239 0.21
22 C31 C C22 N N N 0 8.129 -0.328 0.375
23 C32 C C23 N Y N 0 5.4 1.531 1.69
24 C34 C C24 N Y N 0 4.023 1.459 1.786
25 C36 C C25 N Y N 0 -3.121 -1.841 -1.157
26 C38 C C26 N N N 0 -6.801 -0.384 0.33
27 C39 C C27 N N N 0 -8.15 3.045 -0.371
28 C40 C C28 N N N 0 -8.507 4.171 -1.343
29 F33 F F1 N N N 0 6.116 2.114 2.676
30 N03 N N1 N N N 0 -6.38 1.023 0.184
31 N08 N N2 N N N 0 -5.524 -3.934 1.853
32 N09 N N3 N Y N 0 -4.355 -0.972 0.44
33 N16 N N4 N Y N 0 1.758 -3.524 -1.276
34 N18 N N5 N Y N 0 1.926 -1.302 -0.173
35 N20 N N6 N N N 0 1.895 0.786 0.864
36 N28 N N7 N N N 0 9.966 0.532 -0.999
37 N35 N N8 N Y N 0 -0.105 -0.293 0.332
38 N37 N N9 N Y N 0 -4.358 -1.637 -0.791
39 O01 O O1 N N N 0 -6.908 1.488 -2.146
40 O41 O O2 N N N 0 -5.522 3.061 -0.832
41 S02 S S1 N N N 0 -6.65 2.204 -0.945
42 H101 H H1 N N N 0 -2.742 -0.279 1.711
43 H151 H H2 N N N 0 0.755 -5.254 -2.144
44 H221 H H3 N N N 0 3.371 -0.124 -1.132
45 H261 H H4 N N N 0 7.501 1.41 -1.65
46 H262 H H5 N N N 0 7.56 2.902 -0.68
47 H042 H H6 N N N 0 -6.208 1.224 2.327
48 H041 H H7 N N N 0 -4.656 1.459 1.411
49 H061 H H8 N N N 0 -5.034 -1.14 3.209
50 H062 H H9 N N N 0 -6.773 -1.221 2.837
51 H141 H H10 N N N 0 -1.459 -4.024 -1.525
52 H231 H H11 N N N 0 5.823 0.009 -1.294
53 H251 H H12 N N N 0 7.948 1.578 1.366
54 H272 H H13 N N N 0 9.737 2.461 -1.796
55 H271 H H14 N N N 0 9.891 2.391 -0.024
56 H291 H H15 N N N 0 8.365 -0.233 -2.123
57 H293 H H16 N N N 0 9.697 0.457 -3.081
58 H292 H H17 N N N 0 9.896 -1.125 -2.289
59 H302 H H18 N N N 0 10.079 0.255 1.08
60 H301 H H19 N N N 0 10.062 -1.243 0.12
61 H312 H H20 N N N 0 7.893 -0.887 1.28
62 H311 H H21 N N N 0 7.698 -0.835 -0.489
63 H341 H H22 N N N 0 3.518 1.87 2.648
64 H361 H H23 N N N 0 -2.8 -2.336 -2.062
65 H382 H H24 N N N 0 -6.777 -0.949 -0.601
66 H381 H H25 N N N 0 -7.734 -0.511 0.88
67 H392 H H26 N N N 0 -7.976 3.463 0.621
68 H391 H H27 N N N 0 -8.972 2.331 -0.325
69 H402 H H28 N N N 0 -7.685 4.886 -1.389
70 H403 H H29 N N N 0 -8.682 3.754 -2.335
71 H401 H H30 N N N 0 -9.409 4.677 -0.998
72 H161 H H31 N N N 0 2.69 -3.767 -1.399
73 H201 H H32 N N N 0 1.401 1.494 1.304



Y5D : Chemical Bonds

Total Number of Bonds: 78
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O41 S02 O S doub 1.42 N N
2 O01 S02 O S doub 1.42 N N
3 C39 S02 C S sing 1.81 N N
4 C39 C40 C C sing 1.53 N N
5 S02 N03 S N sing 1.66 N N
6 N03 C38 N C sing 1.48 N N
7 N03 C04 N C sing 1.48 N N
8 C38 C05 C C sing 1.54 N N
9 C04 C05 C C sing 1.54 N N
10 C31 C30 C C sing 1.53 N N
11 C31 C25 C C sing 1.53 N N
12 C30 N28 C N sing 1.47 N N
13 N37 C36 N C doub 1.31 N Y
14 N37 N09 N N sing 1.4 N Y
15 C36 C11 C C sing 1.41 N Y
16 N09 C05 N C sing 1.47 N N
17 N09 C10 N C sing 1.35 N Y
18 F33 C32 F C sing 1.35 N N
19 C05 C06 C C sing 1.53 N N
20 C11 C10 C C doub 1.37 N Y
21 C11 C12 C C sing 1.48 N N
22 C12 N35 C N doub 1.33 N Y
23 C12 C13 C C sing 1.4 N Y
24 C32 C34 C C doub 1.38 N Y
25 C32 C24 C C sing 1.39 N Y
26 C14 C13 C C sing 1.46 N Y
27 C14 C15 C C doub 1.34 N Y
28 C34 C21 C C sing 1.39 N Y
29 C25 C24 C C sing 1.51 N N
30 C25 C26 C C sing 1.53 N N
31 N35 C19 N C sing 1.33 N Y
32 C13 C17 C C doub 1.41 N Y
33 C24 C23 C C doub 1.38 N Y
34 C15 N16 C N sing 1.37 N Y
35 N28 C29 N C sing 1.47 N N
36 N28 C27 N C sing 1.47 N N
37 C21 N20 C N sing 1.4 N N
38 C21 C22 C C doub 1.39 N Y
39 C19 N20 C N sing 1.39 N N
40 C19 N18 C N doub 1.32 N Y
41 C17 N16 C N sing 1.37 N Y
42 C17 N18 C N sing 1.33 N Y
43 C23 C22 C C sing 1.38 N Y
44 C06 C07 C C sing 1.47 N N
45 C26 C27 C C sing 1.53 N N
46 C07 N08 C N trip 1.14 N N
47 C10 H101 C H sing 1.08 N N
48 C15 H151 C H sing 1.08 N N
49 C22 H221 C H sing 1.08 N N
50 C26 H261 C H sing 1.09 N N
51 C26 H262 C H sing 1.09 N N
52 C04 H042 C H sing 1.09 N N
53 C04 H041 C H sing 1.09 N N
54 C06 H061 C H sing 1.09 N N
55 C06 H062 C H sing 1.09 N N
56 C14 H141 C H sing 1.08 N N
57 C23 H231 C H sing 1.08 N N
58 C25 H251 C H sing 1.09 N N
59 C27 H272 C H sing 1.09 N N
60 C27 H271 C H sing 1.09 N N
61 C29 H291 C H sing 1.09 N N
62 C29 H293 C H sing 1.09 N N
63 C29 H292 C H sing 1.09 N N
64 C30 H302 C H sing 1.09 N N
65 C30 H301 C H sing 1.09 N N
66 C31 H312 C H sing 1.09 N N
67 C31 H311 C H sing 1.09 N N
68 C34 H341 C H sing 1.08 N N
69 C36 H361 C H sing 1.08 N N
70 C38 H382 C H sing 1.09 N N
71 C38 H381 C H sing 1.09 N N
72 C39 H392 C H sing 1.09 N N
73 C39 H391 C H sing 1.09 N N
74 C40 H402 C H sing 1.09 N N
75 C40 H403 C H sing 1.09 N N
76 C40 H401 C H sing 1.09 N N
77 N16 H161 N H sing 0.97 N N
78 N20 H201 N H sing 0.97 N N



Y5D : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Y5D 7ll4 Open in New Window Bound ligand 1 1