Chemical Components in the PDB

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XJH : Summary

Code

XJH

One-letter code

X

Molecule name

6-{[(3R,4R)-4-(3-phenoxyphenoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-{[(3R,4R)-4-(3-phenoxyphenoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine
OpenEye OEToolkits 1.7.0 6-[[(3R,4R)-4-(3-phenoxyphenoxy)pyrrolidin-3-yl]methyl]pyridin-2-amine

Formula

C22 H23 N3 O2

Formal charge

0

Molecular weight

361.437 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O(c2cc(Oc1ccccc1)ccc2)C3C(CNC3)Cc4nc(N)ccc4
SMILES CACTVS 3.370 Nc1cccc(C[CH]2CNC[CH]2Oc3cccc(Oc4ccccc4)c3)n1
SMILES OpenEye OEToolkits 1.7.0 c1ccc(cc1)Oc2cccc(c2)OC3CNCC3Cc4cccc(n4)N
Canonical SMILES CACTVS 3.370 Nc1cccc(C[C@@H]2CNC[C@@H]2Oc3cccc(Oc4ccccc4)c3)n1
Canonical SMILES OpenEye OEToolkits 1.7.0 c1ccc(cc1)Oc2cccc(c2)O[C@H]3CNC[C@H]3Cc4cccc(n4)N

IUPAC InChI

InChI=1S/C22H23N3O2/c23-22-11-4-6-17(25-22)12-16-14-24-15-21(16)27-20-10-5-9-19(13-20)26-18-7-2-1-3-8-18/h1-11,13,16,21,24H,12,14-15H2,(H2,23,25)/t16-,21+/m1/s1

IUPAC InChI key

MKBQBMWQPUXDQQ-IERDGZPVSA-N
XJH

wwPDB Information

Atom count

50 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-06-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



XJH : 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 N01 N N01 N Y N 0 -4.891 0.975 -0.772
2 C02 C C02 N Y N 0 -6.138 1.415 -0.838
3 N02 N N02 N N N 0 -6.764 1.532 -2.074
4 C03 C C03 N Y N 0 -6.829 1.761 0.319
5 C04 C C04 N Y N 0 -6.195 1.64 1.542
6 C05 C C05 N Y N 0 -4.887 1.174 1.567
7 C06 C C06 N Y N 0 -4.262 0.849 0.38
8 C07 C C07 N N N 0 -2.842 0.343 0.401
9 N1' N N1' N N N 0 -2.75 -3.316 0.309
10 O10 O O10 N N N 0 -0.446 -0.586 0.295
11 C11 C C11 N Y N 0 0.872 -0.64 -0.033
12 C12 C C12 N Y N 0 1.309 -1.527 -1.006
13 C13 C C13 N Y N 0 2.649 -1.582 -1.339
14 C14 C C14 N Y N 0 3.556 -0.755 -0.705
15 C15 C C15 N Y N 0 3.123 0.134 0.269
16 C16 C C16 N Y N 0 1.778 0.195 0.601
17 C2' C C2' N N N 0 -3.553 -2.077 0.466
18 O20 O O20 N N N 0 4.015 0.947 0.893
19 C21 C C21 N Y N 0 5.303 0.932 0.46
20 C22 C C22 N Y N 0 5.626 1.465 -0.781
21 C23 C C23 N Y N 0 6.936 1.448 -1.219
22 C24 C C24 N Y N 0 7.925 0.901 -0.423
23 C25 C C25 N Y N 0 7.607 0.369 0.813
24 C26 C C26 N Y N 0 6.299 0.389 1.259
25 C3' C C3' R N N 0 -2.77 -1.004 -0.321
26 C4' C C4' R N N 0 -1.315 -1.515 -0.357
27 C5' C C5' N N N 0 -1.341 -2.854 0.411
28 HN02 H HN02 N N N 0 -6.286 1.291 -2.884
29 HN0A H HN0A N N N 0 -7.677 1.854 -2.127
30 H03 H H03 N N N 0 -7.846 2.12 0.263
31 H04 H H04 N N N 0 -6.705 1.901 2.457
32 H05 H H05 N N N 0 -4.364 1.067 2.506
33 H07 H H07 N N N 0 -2.194 1.06 -0.102
34 H07A H H07A N N N 0 -2.516 0.22 1.434
35 HN1' H HN1' N N N 0 -2.965 -3.981 1.037
36 H12 H H12 N N N 0 0.603 -2.175 -1.503
37 H13 H H13 N N N 0 2.988 -2.273 -2.097
38 H14 H H14 N N N 0 4.603 -0.8 -0.967
39 H16 H H16 N N N 0 1.439 0.889 1.356
40 H2' H H2' N N N 0 -4.547 -2.211 0.039
41 H2'A H H2'A N N N 0 -3.625 -1.8 1.518
42 H22 H H22 N N N 0 4.853 1.891 -1.403
43 H23 H H23 N N N 0 7.187 1.862 -2.184
44 H24 H H24 N N N 0 8.949 0.889 -0.767
45 H25 H H25 N N N 0 8.381 -0.058 1.433
46 H26 H H26 N N N 0 6.051 -0.026 2.224
47 H3' H H3' N N N 0 -3.166 -0.912 -1.332
48 H4' H H4' N N N 0 -0.995 -1.674 -1.387
49 H5' H H5' N N N 0 -1.067 -2.699 1.454
50 H5'A H H5'A N N N 0 -0.67 -3.574 -0.057



XJH : 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 N01 C N doub 1.32 N Y
2 C06 N01 C N sing 1.32 N Y
3 C03 C02 C C sing 1.39 N Y
4 C02 N02 C N sing 1.39 N N
5 N02 HN02 N H sing 0.97 N N
6 N02 HN0A N H sing 0.97 N N
7 C04 C03 C C doub 1.38 N Y
8 C03 H03 C H sing 1.08 N N
9 C04 C05 C C sing 1.39 N Y
10 C04 H04 C H sing 1.08 N N
11 C05 C06 C C doub 1.38 N Y
12 C05 H05 C H sing 1.08 N N
13 C06 C07 C C sing 1.51 N N
14 C07 C3' C C sing 1.53 N N
15 C07 H07 C H sing 1.09 N N
16 C07 H07A C H sing 1.09 N N
17 C2' N1' C N sing 1.48 N N
18 N1' C5' N C sing 1.49 N N
19 N1' HN1' N H sing 1.01 N N
20 O10 C4' O C sing 1.43 N N
21 O10 C11 O C sing 1.36 N N
22 C12 C11 C C doub 1.39 N Y
23 C11 C16 C C sing 1.39 N Y
24 C12 C13 C C sing 1.38 N Y
25 C12 H12 C H sing 1.08 N N
26 C13 C14 C C doub 1.38 N Y
27 C13 H13 C H sing 1.08 N N
28 C14 C15 C C sing 1.39 N Y
29 C14 H14 C H sing 1.08 N N
30 C16 C15 C C doub 1.39 N Y
31 C15 O20 C O sing 1.36 N N
32 C16 H16 C H sing 1.08 N N
33 C2' C3' C C sing 1.54 N N
34 C2' H2' C H sing 1.09 N N
35 C2' H2'A C H sing 1.09 N N
36 O20 C21 O C sing 1.36 N N
37 C26 C21 C C doub 1.39 N Y
38 C21 C22 C C sing 1.39 N Y
39 C23 C22 C C doub 1.38 N Y
40 C22 H22 C H sing 1.08 N N
41 C24 C23 C C sing 1.38 N Y
42 C23 H23 C H sing 1.08 N N
43 C25 C24 C C doub 1.38 N Y
44 C24 H24 C H sing 1.08 N N
45 C25 C26 C C sing 1.38 N Y
46 C25 H25 C H sing 1.08 N N
47 C26 H26 C H sing 1.08 N N
48 C3' C4' C C sing 1.54 N N
49 C3' H3' C H sing 1.09 N N
50 C5' C4' C C sing 1.54 N N
51 C4' H4' C H sing 1.09 N N
52 C5' H5' C H sing 1.09 N N
53 C5' H5'A C H sing 1.09 N N



XJH : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XJH 3n2r Open in New Window Bound ligand 2 1