Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

EXI : Summary

Code

EXI

One-letter code

X

Molecule name

N1-(5-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-3-yl)-N1,N2-dimethylethane-1,2-diamine

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 N'-[5-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]pyridin-3-yl]-N,N'-dimethyl-ethane-1,2-diamine

Formula

C17 H25 N5

Formal charge

0

Molecular weight

299.414 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CNCCN(C)c1cncc(CCc2cc(C)cc(N)n2)c1
SMILES OpenEye OEToolkits 1.7.6 Cc1cc(nc(c1)N)CCc2cc(cnc2)N(C)CCNC
Canonical SMILES CACTVS 3.385 CNCCN(C)c1cncc(CCc2cc(C)cc(N)n2)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1cc(nc(c1)N)CCc2cc(cnc2)N(C)CCNC

IUPAC InChI

InChI=1S/C17H25N5/c1-13-8-15(21-17(18)9-13)5-4-14-10-16(12-20-11-14)22(3)7-6-19-2/h8-12,19H,4-7H2,1-3H3,(H2,18,21)

IUPAC InChI key

BAILAIZRWKFZJT-UHFFFAOYSA-N
EXI

wwPDB Information

Atom count

47 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-03-23

Last modified at

2015-06-19

Status

Released

Obsoleted

Not Assigned



EXI : 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 N01 N N01 N Y N 0 -3.687 -1.071 0.158
2 C02 C C02 N Y N 0 -4.929 -1.456 0.408
3 N02 N N02 N N N 0 -5.17 -2.742 0.876
4 C03 C C03 N Y N 0 -5.995 -0.584 0.208
5 C04 C C04 N Y N 0 -5.74 0.693 -0.257
6 C05 C C05 N Y N 0 -4.424 1.058 -0.507
7 C06 C C06 N Y N 0 -3.415 0.142 -0.287
8 C07 C C07 N N N 0 -6.866 1.668 -0.487
9 C08 C C08 N N N 0 -1.985 0.531 -0.557
10 C09 C C09 N N N 0 -1.145 0.294 0.7
11 N11 N N11 N Y N 0 1.965 2.328 0.438
12 C12 C C12 N Y N 0 0.715 1.976 0.67
13 C13 C C13 N Y N 0 0.285 0.684 0.43
14 C14 C C14 N Y N 0 1.184 -0.249 -0.061
15 C15 C C15 N Y N 0 2.496 0.157 -0.295
16 C16 C C16 N Y N 0 2.852 1.473 -0.029
17 C17 C C17 N N N 0 3.053 -2.132 -1.066
18 N17 N N17 N N N 0 3.44 -0.747 -0.789
19 C18 C C18 N N N 0 4.817 -0.309 -1.032
20 C19 C C19 N N N 0 5.65 -0.524 0.233
21 N20 N N20 N N N 0 7.031 -0.085 -0.01
22 C21 C C21 N N N 0 7.863 -0.278 1.186
23 HN02 H HN02 N N N 0 -4.43 -3.354 1.017
24 HN0A H HN0A N N N 0 -6.078 -3.029 1.061
25 H03 H H03 N N N 0 -7.007 -0.9 0.413
26 H05 H H05 N N N 0 -4.192 2.048 -0.872
27 H07 H H07 N N N 0 -7.047 2.237 0.425
28 H07A H H07A N N N 0 -6.598 2.35 -1.294
29 H07B H H07B N N N 0 -7.77 1.122 -0.759
30 H08 H H08 N N N 0 -1.592 -0.073 -1.375
31 H08A H H08A N N N 0 -1.941 1.585 -0.83
32 H09 H H09 N N N 0 -1.538 0.898 1.518
33 H09A H H09A N N N 0 -1.19 -0.76 0.973
34 H12 H H12 N N N 0 0.018 2.707 1.053
35 H14 H H14 N N N 0 0.876 -1.265 -0.257
36 H16 H H16 N N N 0 3.866 1.798 -0.206
37 H17 H H17 N N N 0 2.704 -2.214 -2.095
38 H17A H H17A N N N 0 3.913 -2.786 -0.92
39 H17B H H17B N N N 0 2.253 -2.428 -0.387
40 H18 H H18 N N N 0 5.243 -0.888 -1.851
41 H18A H H18A N N N 0 4.821 0.749 -1.294
42 H19 H H19 N N N 0 5.224 0.054 1.052
43 H19A H H19A N N N 0 5.646 -1.582 0.495
44 HN20 H HN20 N N N 0 7.427 -0.561 -0.807
45 H21 H H21 N N N 0 8.88 0.056 0.978
46 H21A H H21A N N N 0 7.451 0.303 2.011
47 H21B H H21B N N N 0 7.874 -1.334 1.454



EXI : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N01 C02 N C doub 1.32 N Y
2 N01 C06 N C sing 1.32 N Y
3 C02 N02 C N sing 1.39 N N
4 C02 C03 C C sing 1.39 N Y
5 C03 C04 C C doub 1.38 N Y
6 C04 C05 C C sing 1.39 N Y
7 C04 C07 C C sing 1.51 N N
8 C05 C06 C C doub 1.38 N Y
9 C06 C08 C C sing 1.51 N N
10 C08 C09 C C sing 1.53 N N
11 C09 C13 C C sing 1.51 N N
12 N11 C12 N C doub 1.32 N Y
13 N11 C16 N C sing 1.32 N Y
14 C12 C13 C C sing 1.38 N Y
15 C13 C14 C C doub 1.39 N Y
16 C14 C15 C C sing 1.39 N Y
17 C15 C16 C C doub 1.39 N Y
18 C15 N17 C N sing 1.4 N N
19 C17 N17 C N sing 1.46 N N
20 N17 C18 N C sing 1.47 N N
21 C18 C19 C C sing 1.53 N N
22 C19 N20 C N sing 1.47 N N
23 N20 C21 N C sing 1.47 N N
24 N02 HN02 N H sing 0.97 N N
25 N02 HN0A N H sing 0.97 N N
26 C03 H03 C H sing 1.08 N N
27 C05 H05 C H sing 1.08 N N
28 C07 H07 C H sing 1.09 N N
29 C07 H07A C H sing 1.09 N N
30 C07 H07B C H sing 1.09 N N
31 C08 H08 C H sing 1.09 N N
32 C08 H08A C H sing 1.09 N N
33 C09 H09 C H sing 1.09 N N
34 C09 H09A C H sing 1.09 N N
35 C12 H12 C H sing 1.08 N N
36 C14 H14 C H sing 1.08 N N
37 C16 H16 C H sing 1.08 N N
38 C17 H17 C H sing 1.09 N N
39 C17 H17A C H sing 1.09 N N
40 C17 H17B C H sing 1.09 N N
41 C18 H18 C H sing 1.09 N N
42 C18 H18A C H sing 1.09 N N
43 C19 H19 C H sing 1.09 N N
44 C19 H19A C H sing 1.09 N N
45 N20 HN20 N H sing 1.01 N N
46 C21 H21 C H sing 1.09 N N
47 C21 H21A C H sing 1.09 N N
48 C21 H21B C H sing 1.09 N N



EXI : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
EXI 4ugy Open in New Window Bound ligand 1 1
EXI 4uh1 Open in New Window Bound ligand 2 1
EXI 4uh5 Open in New Window Bound ligand 2 1
EXI 4uh8 Open in New Window Bound ligand 2 1
EXI 5g0n Open in New Window Bound ligand 2 1