Chemical Components in the PDB

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HW0 : Summary

Code

HW0

One-letter code

X

Molecule name

6-{[(3R,4R)-4-{[5-(6-aminopyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-{[(3R,4R)-4-{[5-(6-aminopyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
OpenEye OEToolkits 1.7.6 6-[[(3R,4R)-4-[5-(6-azanylpyridin-2-yl)pentoxy]pyrrolidin-3-yl]methyl]-4-methyl-pyridin-2-amine

Formula

C21 H31 N5 O

Formal charge

0

Molecular weight

369.504 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O(CCCCCc1nc(N)ccc1)C2C(CNC2)Cc3nc(N)cc(c3)C
SMILES CACTVS 3.370 Cc1cc(N)nc(C[CH]2CNC[CH]2OCCCCCc3cccc(N)n3)c1
SMILES OpenEye OEToolkits 1.7.6 Cc1cc(nc(c1)N)CC2CNCC2OCCCCCc3cccc(n3)N
Canonical SMILES CACTVS 3.370 Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCCCCc3cccc(N)n3)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1cc(nc(c1)N)C[C@@H]2CNC[C@@H]2OCCCCCc3cccc(n3)N

IUPAC InChI

InChI=1S/C21H31N5O/c1-15-10-18(26-21(23)11-15)12-16-13-24-14-19(16)27-9-4-2-3-6-17-7-5-8-20(22)25-17/h5,7-8,10-11,16,19,24H,2-4,6,9,12-14H2,1H3,(H2,22,25)(H2,23,26)/t16-,19+/m1/s1

IUPAC InChI key

ISEYRPTZYRJQPZ-APWZRJJASA-N
HW0

wwPDB Information

Atom count

58 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-11-23

Last modified at

2012-07-06

Status

Released

Obsoleted

Not Assigned



HW0 : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N22 N N22 N N N 0 7.075 3.353 -0.187
2 C22 C C22 N Y N 0 7.223 1.982 -0.011
3 C23 C C23 N Y N 0 8.37 1.484 0.598
4 C24 C C24 N Y N 0 8.504 0.118 0.766
5 C25 C C25 N Y N 0 7.481 -0.708 0.319
6 N21 N N21 N Y N 0 6.267 1.162 -0.419
7 C26 C C26 N Y N 0 6.37 -0.146 -0.276
8 C14 C C14 N N N 0 5.256 -1.037 -0.764
9 C13 C C13 N N N 0 3.935 -0.595 -0.132
10 C12 C C12 N N N 0 2.805 -1.5 -0.627
11 C11 C C11 N N N 0 1.484 -1.058 0.005
12 C10 C C10 N N N 0 0.354 -1.963 -0.49
13 O09 O O09 N N N 0 -0.881 -1.55 0.1
14 C4' C C4' R N N 0 -2.007 -2.335 -0.298
15 C5' C C5' N N N 0 -2.264 -3.462 0.724
16 N1' N N1' N N N 0 -3.743 -3.568 0.8
17 C2' C C2' N N N 0 -4.213 -2.16 0.75
18 C3' C C3' R N N 0 -3.289 -1.478 -0.281
19 C08 C C08 N N N 0 -2.967 -0.048 0.157
20 C06 C C06 N Y N 0 -4.207 0.802 0.05
21 N01 N N01 N Y N 0 -4.854 0.868 -1.098
22 C02 C C02 N Y N 0 -5.948 1.601 -1.238
23 N02 N N02 N N N 0 -6.597 1.642 -2.467
24 C03 C C03 N Y N 0 -6.452 2.331 -0.167
25 C04 C C04 N Y N 0 -5.796 2.282 1.049
26 C05 C C05 N Y N 0 -4.655 1.496 1.156
27 C07 C C07 N N N 0 -6.31 3.058 2.234
28 H1 H H1 N N N 0 6.275 3.705 -0.607
29 H2 H H2 N N N 0 7.771 3.958 0.114
30 H3 H H3 N N N 0 9.147 2.156 0.933
31 H4 H H4 N N N 0 9.384 -0.297 1.235
32 H5 H H5 N N N 0 7.554 -1.779 0.435
33 H6 H H6 N N N 0 5.182 -0.965 -1.849
34 H7 H H7 N N N 0 5.467 -2.069 -0.482
35 H8 H H8 N N N 0 4.009 -0.667 0.953
36 H9 H H9 N N N 0 3.724 0.436 -0.414
37 H10 H H10 N N N 0 2.731 -1.428 -1.712
38 H11 H H11 N N N 0 3.016 -2.532 -0.345
39 H12 H H12 N N N 0 1.558 -1.13 1.09
40 H13 H H13 N N N 0 1.273 -0.026 -0.277
41 H14 H H14 N N N 0 0.279 -1.891 -1.575
42 H15 H H15 N N N 0 0.564 -2.995 -0.208
43 H16 H H16 N N N 0 -1.844 -2.752 -1.292
44 H17 H H17 N N N 0 -1.833 -4.4 0.373
45 H18 H H18 N N N 0 -1.851 -3.194 1.697
46 H19 H H19 N N N 0 -4.108 -4.099 0.023
47 H21 H H21 N N N 0 -5.251 -2.117 0.418
48 H22 H H22 N N N 0 -4.108 -1.689 1.728
49 H23 H H23 N N N 0 -3.757 -1.477 -1.266
50 H24 H H24 N N N 0 -2.62 -0.054 1.191
51 H28 H H28 N N N 0 -7.344 2.929 -0.284
52 H25 H H25 N N N 0 -2.189 0.363 -0.485
53 H26 H H26 N N N 0 -6.249 1.135 -3.216
54 H27 H H27 N N N 0 -7.398 2.178 -2.574
55 H29 H H29 N N N 0 -4.122 1.433 2.093
56 H30 H H30 N N N 0 -7.009 2.44 2.798
57 H31 H H31 N N N 0 -5.474 3.338 2.876
58 H32 H H32 N N N 0 -6.818 3.957 1.887



HW0 : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C24 C23 C C doub 1.38 N Y
2 C24 C25 C C sing 1.39 N Y
3 C23 C22 C C sing 1.39 N Y
4 C25 C26 C C doub 1.38 N Y
5 C22 N22 C N sing 1.39 N N
6 C22 N21 C N doub 1.32 N Y
7 C12 C13 C C sing 1.53 N N
8 C12 C11 C C sing 1.53 N N
9 C26 N21 C N sing 1.32 N Y
10 C26 C14 C C sing 1.51 N N
11 C14 C13 C C sing 1.53 N N
12 C11 C10 C C sing 1.53 N N
13 C10 O09 C O sing 1.43 N N
14 O09 C4' O C sing 1.43 N N
15 C08 C06 C C sing 1.51 N N
16 C08 C3' C C sing 1.53 N N
17 C4' C3' C C sing 1.54 N N
18 C4' C5' C C sing 1.54 N N
19 C06 N01 C N doub 1.32 N Y
20 C06 C05 C C sing 1.38 N Y
21 N01 C02 N C sing 1.32 N Y
22 C05 C04 C C doub 1.39 N Y
23 C3' C2' C C sing 1.54 N N
24 C02 N02 C N sing 1.39 N N
25 C02 C03 C C doub 1.39 N Y
26 C5' N1' C N sing 1.48 N N
27 C04 C03 C C sing 1.38 N Y
28 C04 C07 C C sing 1.51 N N
29 C2' N1' C N sing 1.49 N N
30 N22 H1 N H sing 0.97 N N
31 N22 H2 N H sing 0.97 N N
32 C23 H3 C H sing 1.08 N N
33 C24 H4 C H sing 1.08 N N
34 C25 H5 C H sing 1.08 N N
35 C14 H6 C H sing 1.09 N N
36 C14 H7 C H sing 1.09 N N
37 C13 H8 C H sing 1.09 N N
38 C13 H9 C H sing 1.09 N N
39 C12 H10 C H sing 1.09 N N
40 C12 H11 C H sing 1.09 N N
41 C11 H12 C H sing 1.09 N N
42 C11 H13 C H sing 1.09 N N
43 C10 H14 C H sing 1.09 N N
44 C10 H15 C H sing 1.09 N N
45 C4' H16 C H sing 1.09 N N
46 C5' H17 C H sing 1.09 N N
47 C5' H18 C H sing 1.09 N N
48 N1' H19 N H sing 1.01 N N
49 C2' H21 C H sing 1.09 N N
50 C2' H22 C H sing 1.09 N N
51 C3' H23 C H sing 1.09 N N
52 C08 H24 C H sing 1.09 N N
53 C08 H25 C H sing 1.09 N N
54 N02 H26 N H sing 0.97 N N
55 N02 H27 N H sing 0.97 N N
56 C03 H28 C H sing 1.08 N N
57 C05 H29 C H sing 1.08 N N
58 C07 H30 C H sing 1.09 N N
59 C07 H31 C H sing 1.09 N N
60 C07 H32 C H sing 1.09 N N



HW0 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
HW0 3ufw Open in New Window Bound ligand 2 1
HW0 4cwx Open in New Window Bound ligand 2 1