Chemical Components in the PDB

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M04 : Summary

Code

M04

One-letter code

X

Molecule name

1-[4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine

Systematic names

ProgramVersionName
ACDLabs 10.04 1-[4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine
OpenEye OEToolkits 1.5.0 [4-[(4-chlorophenyl)methyl]-1-(7H-pyrrolo[3,2-e]pyrimidin-4-yl)piperidin-4-yl]methanamine

Formula

C19 H22 Cl N5

Formal charge

0

Molecular weight

355.864 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Clc1ccc(cc1)CC4(CCN(c2ncnc3c2ccn3)CC4)CN
SMILES CACTVS 3.341 NCC1(CCN(CC1)c2ncnc3[nH]ccc23)Cc4ccc(Cl)cc4
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1CC2(CCN(CC2)c3c4cc[nH]c4ncn3)CN)Cl
Canonical SMILES CACTVS 3.341 NCC1(CCN(CC1)c2ncnc3[nH]ccc23)Cc4ccc(Cl)cc4
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1CC2(CCN(CC2)c3c4cc[nH]c4ncn3)CN)Cl

IUPAC InChI

InChI=1S/C19H22ClN5/c20-15-3-1-14(2-4-15)11-19(12-21)6-9-25(10-7-19)18-16-5-8-22-17(16)23-13-24-18/h1-5,8,13H,6-7,9-12,21H2,(H,22,23,24)

IUPAC InChI key

KCWPSUKJCKZEAO-UHFFFAOYSA-N
M04

wwPDB Information

Atom count

47 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

Is modified

No

Standard parent

Not Assigned

Defined at

2008-02-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



M04 : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 7.383 9.83 3.238
2 C2 C C2 N N N 0 8.005 8.922 2.259
3 C3 C C3 N N N 0 9.463 9.277 2.0
4 C5 C C5 N N N 0 10.29 7.913 3.967
5 N6 N N6 N N N 0 10.967 6.884 3.131
6 C7 C C7 N N N 0 9.601 10.282 4.235
7 C8 C C8 N N N 0 8.142 9.929 4.496
8 C9 C C9 N Y N 0 12.018 10.831 2.104
9 C10 C C10 N Y N 0 12.216 10.579 0.755
10 C11 C C11 N Y N 0 12.503 11.611 -0.115
11 C12 C C12 N Y N 0 12.602 12.906 0.354
12 CL1 CL CL1 N N N 0 13.016 14.193 -0.734
13 C14 C C14 N Y N 0 12.426 13.162 1.702
14 C15 C C15 N Y N 0 12.138 12.13 2.57
15 C16 C C16 N Y N 0 5.956 9.786 3.408
16 N17 N N17 N Y N 0 5.49 9.858 4.668
17 C13 C C13 N N N 0 11.757 9.698 3.059
18 C18 C C18 N Y N 0 4.166 9.827 4.851
19 N19 N N19 N Y N 0 3.201 9.721 3.936
20 C20 C C20 N Y N 0 3.699 9.653 2.694
21 N21 N N21 N Y N 0 2.971 9.529 1.547
22 C22 C C22 N Y N 0 3.804 9.503 0.478
23 C23 C C23 N Y N 0 5.096 9.598 0.93
24 C24 C C24 N Y N 0 5.038 9.698 2.353
25 C4 C C4 N N N 0 10.292 9.295 3.286
26 H2C1 H 1H2C N N N 0 7.957 7.895 2.651
27 H2C2 H 2H2C N N N 0 7.457 9.015 1.31
28 H8C1 H 1H8C N N N 0 7.693 10.714 5.122
29 H8C2 H 2H8C N N N 0 8.105 8.954 5.003
30 H3C1 H 1H3C N N N 0 9.89 8.527 1.319
31 H3C2 H 2H3C N N N 0 9.493 10.286 1.563
32 H5C1 H 1H5C N N N 0 9.248 7.603 4.133
33 H5C2 H 2H5C N N N 0 10.838 7.998 4.917
34 H6N1 H 1H6N N N N 0 11.119 7.248 2.212
35 H6N2 H 2H6N N N N 0 11.846 6.645 3.544
36 H7C1 H 1H7C N N N 0 9.639 11.283 3.781
37 H7C2 H 2H7C N N N 0 10.13 10.243 5.199
38 H10 H H10 N N N 0 12.145 9.568 0.382
39 H15 H H15 N N N 0 12.005 12.336 3.622
40 H131 H 1H13 N N N 0 12.275 8.814 2.658
41 H132 H 2H13 N N N 0 12.112 10.057 4.036
42 H11 H H11 N N N 0 12.651 11.405 -1.165
43 H14 H H14 N N N 0 12.514 14.172 2.075
44 H18 H H18 N N N 0 3.833 9.897 5.876
45 H21 H H21 N N N 0 1.974 9.467 1.502
46 H22 H H22 N N N 0 3.502 9.421 -0.556
47 H23 H H23 N N N 0 5.989 9.597 0.323



M04 : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.47 N N
2 N1 C8 N C sing 1.47 N N
3 N1 C16 N C sing 1.44 N N
4 C2 C3 C C sing 1.52 N N
5 C3 C4 C C sing 1.53 N N
6 C5 N6 C N sing 1.49 N N
7 C5 C4 C C sing 1.54 N N
8 C7 C8 C C sing 1.52 N N
9 C7 C4 C C sing 1.53 N N
10 C9 C10 C C sing 1.39 N Y
11 C9 C15 C C doub 1.39 N Y
12 C9 C13 C C sing 1.5 N N
13 C10 C11 C C doub 1.38 N Y
14 C11 C12 C C sing 1.38 N Y
15 C12 CL1 C CL sing 1.74 N N
16 C12 C14 C C doub 1.38 N Y
17 C14 C15 C C sing 1.38 N Y
18 C16 N17 C N sing 1.35 N Y
19 C16 C24 C C doub 1.4 N Y
20 N17 C18 N C doub 1.34 N Y
21 C18 N19 C N sing 1.33 N Y
22 C13 C4 C C sing 1.54 N N
23 N19 C20 N C doub 1.34 N Y
24 C20 N21 C N sing 1.36 N Y
25 C20 C24 C C sing 1.38 N Y
26 N21 C22 N C sing 1.36 N Y
27 C22 C23 C C doub 1.37 N Y
28 C23 C24 C C sing 1.43 N Y
29 C2 H2C1 C H sing 1.1 N N
30 C2 H2C2 C H sing 1.1 N N
31 C8 H8C1 C H sing 1.1 N N
32 C8 H8C2 C H sing 1.1 N N
33 C3 H3C1 C H sing 1.1 N N
34 C3 H3C2 C H sing 1.1 N N
35 C5 H5C1 C H sing 1.1 N N
36 C5 H5C2 C H sing 1.1 N N
37 N6 H6N1 N H sing 1.0 N N
38 N6 H6N2 N H sing 1.0 N N
39 C7 H7C1 C H sing 1.1 N N
40 C7 H7C2 C H sing 1.1 N N
41 C10 H10 C H sing 1.08 N N
42 C15 H15 C H sing 1.08 N N
43 C13 H131 C H sing 1.1 N N
44 C13 H132 C H sing 1.1 N N
45 C11 H11 C H sing 1.08 N N
46 C14 H14 C H sing 1.08 N N
47 C18 H18 C H sing 1.08 N N
48 N21 H21 N H sing 1.0 N N
49 C22 H22 C H sing 1.08 N N
50 C23 H23 C H sing 1.08 N N



M04 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
M04 2vo3 Open in New Window Bound ligand 1 1