Chemical Components in the PDB

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5XH : Summary

Code

5XH

One-letter code

X

Molecule name

~{N}-[1-[(3~{R})-1-[4-(dimethylamino)but-2-enoyl]azepan-3-yl]-7-methyl-benzimidazol-2-yl]-2-methyl-pyridine-4-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.4 ~{N}-[1-[(3~{R})-1-[4-(dimethylamino)but-2-enoyl]azepan-3-yl]-7-methyl-benzimidazol-2-yl]-2-methyl-pyridine-4-carboxamide

Formula

C27 H34 N6 O2

Formal charge

0

Molecular weight

474.598 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(C)CC=CC(=O)N1CCCC[CH](C1)n2c(NC(=O)c3ccnc(C)c3)nc4cccc(C)c24
SMILES OpenEye OEToolkits 2.0.4 Cc1cccc2c1n(c(n2)NC(=O)c3ccnc(c3)C)C4CCCCN(C4)C(=O)C=CCN(C)C
Canonical SMILES CACTVS 3.385 CN(C)C/C=C/C(=O)N1CCCC[C@H](C1)n2c(NC(=O)c3ccnc(C)c3)nc4cccc(C)c24
Canonical SMILES OpenEye OEToolkits 2.0.4 Cc1cccc2c1n(c(n2)NC(=O)c3ccnc(c3)C)[C@@H]4CCCCN(C4)C(=O)C=CCN(C)C

IUPAC InChI

InChI=1S/C27H34N6O2/c1-19-9-7-11-23-25(19)33(27(29-23)30-26(35)21-13-14-28-20(2)17-21)22-10-5-6-16-32(18-22)24(34)12-8-15-31(3)4/h7-9,11-14,17,22H,5-6,10,15-16,18H2,1-4H3,(H,29,30,35)/b12-8+/t22-/m1/s1

IUPAC InChI key

SKLAQDNYYXAFGK-QWDXWUACSA-N
5XH

wwPDB Information

Atom count

69 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-12-21

Last modified at

2016-07-22

Status

Released

Obsoleted

Not Assigned



5XH : Atoms of Molecule

Total Number of Atoms: 69
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 6.438 2.386 1.775
2 C2 C C2 N N N 0 5.856 1.395 -0.356
3 C3 C C3 N N N 0 4.508 0.929 0.13
4 O1 O O1 N N N 0 -2.532 -3.104 0.299
5 O2 O O2 N N N 0 2.012 0.163 0.98
6 C11 C C4 N Y N 0 -2.507 -0.46 0.098
7 C12 C C5 N N N 0 -1.464 -2.582 0.043
8 C13 C C6 N Y N 0 -0.256 -3.42 -0.141
9 C14 C C7 N Y N 0 0.982 -2.84 -0.436
10 C15 C C8 N Y N 0 2.082 -3.659 -0.599
11 C16 C C9 N Y N 0 0.83 -5.554 -0.198
12 C17 C C10 N N N 0 0.773 -7.055 -0.076
13 C18 C C11 N Y N 0 -0.321 -4.811 -0.019
14 C19 C C12 N Y N 0 -4.574 0.122 0.475
15 C20 C C13 N Y N 0 -5.942 0.204 0.747
16 C21 C C14 N Y N 0 -6.56 1.433 0.782
17 C22 C C15 N Y N 0 -5.834 2.593 0.549
18 C23 C C16 N Y N 0 -4.483 2.529 0.28
19 C24 C C17 N N N 0 -3.703 3.793 0.027
20 C25 C C18 N Y N 0 -3.845 1.298 0.237
21 C26 C C19 N N N 0 -0.277 1.519 0.71
22 C27 C C20 N N N 0 8.181 1.607 0.285
23 C5 C C21 N N N 0 2.118 1.234 0.414
24 C4 C C22 N N N 0 3.434 1.689 -0.06
25 N1 N N1 N N N 0 6.809 1.389 0.762
26 N2 N N2 N N N 0 1.028 2.005 0.222
27 C10 C C23 R N N 0 -1.406 1.778 -0.303
28 C9 C C24 N N N 0 -0.919 1.501 -1.704
29 C8 C C25 N N N 0 -0.374 2.789 -2.314
30 C7 C C26 N N N 0 1.03 3.071 -1.979
31 C6 C C27 N N N 0 1.187 3.272 -0.454
32 N3 N N3 N Y N 0 -2.54 0.901 -0.001
33 N6 N N4 N Y N 0 -3.703 -0.916 0.375
34 N4 N N5 N N N 0 -1.379 -1.242 -0.073
35 N5 N N6 N Y N 0 1.976 -4.967 -0.481
36 H1 H H1 N N N 0 6.504 3.385 1.342
37 H2 H H2 N N N 0 5.418 2.202 2.11
38 H3 H H3 N N N 0 7.119 2.313 2.623
39 H4 H H4 N N N 0 6.211 0.725 -1.14
40 H5 H H5 N N N 0 5.769 2.406 -0.754
41 H6 H H6 N N N 0 4.415 -0.023 0.632
42 H8 H H8 N N N 0 1.076 -1.769 -0.534
43 H9 H H9 N N N 0 3.043 -3.221 -0.827
44 H10 H H10 N N N 0 0.968 -7.343 0.957
45 H11 H H11 N N N 0 -0.216 -7.406 -0.37
46 H12 H H12 N N N 0 1.525 -7.501 -0.726
47 H13 H H13 N N N 0 -1.257 -5.298 0.213
48 H14 H H14 N N N 0 -6.514 -0.695 0.929
49 H15 H H15 N N N 0 -7.617 1.496 0.993
50 H16 H H16 N N N 0 -6.331 3.551 0.579
51 H17 H H17 N N N 0 -3.202 4.101 0.945
52 H18 H H18 N N N 0 -2.96 3.613 -0.749
53 H19 H H19 N N N 0 -4.383 4.581 -0.297
54 H20 H H20 N N N 0 -0.208 0.447 0.898
55 H21 H H21 N N N 0 -0.517 2.027 1.645
56 H22 H H22 N N N 0 8.866 1.598 1.133
57 H23 H H23 N N N 0 8.454 0.814 -0.411
58 H24 H H24 N N N 0 8.242 2.571 -0.22
59 H25 H H25 N N N 0 3.527 2.641 -0.563
60 H28 H H28 N N N 0 -1.725 2.818 -0.232
61 H29 H H29 N N N 0 -0.129 0.751 -1.673
62 H30 H H30 N N N 0 -1.746 1.133 -2.311
63 H31 H H31 N N N 0 -0.465 2.724 -3.398
64 H32 H H32 N N N 0 -0.986 3.622 -1.968
65 H33 H H33 N N N 0 1.651 2.235 -2.3
66 H34 H H34 N N N 0 0.429 3.971 -0.1
67 H35 H H35 N N N 0 -0.527 -0.826 -0.278
68 H7 H H7 N N N 0 1.35 3.975 -2.497
69 H26 H H26 N N N 0 2.178 3.675 -0.242



5XH : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N1 C N sing 1.47 N N
2 C27 N1 C N sing 1.47 N N
3 N1 C2 N C sing 1.47 N N
4 C8 C7 C C sing 1.47 N N
5 C8 C9 C C sing 1.53 N N
6 C24 C23 C C sing 1.51 N N
7 C2 C3 C C sing 1.51 N N
8 C7 C6 C C sing 1.55 N N
9 C4 C3 C C doub 1.33 E N
10 C4 C5 C C sing 1.47 N N
11 C9 C10 C C sing 1.51 N N
12 C10 N3 C N sing 1.47 N N
13 C10 C26 C C sing 1.54 N N
14 C23 C22 C C doub 1.38 N Y
15 C23 C25 C C sing 1.39 N Y
16 C6 N2 C N sing 1.44 N N
17 C5 N2 C N sing 1.35 N N
18 C5 O2 C O doub 1.22 N N
19 N2 C26 N C sing 1.48 N N
20 C22 C21 C C sing 1.39 N Y
21 N3 C25 N C sing 1.38 N Y
22 N3 C11 N C sing 1.36 N Y
23 C25 C19 C C doub 1.4 N Y
24 C21 C20 C C doub 1.38 N Y
25 C11 N4 C N sing 1.38 N N
26 C11 N6 C N doub 1.31 N Y
27 C19 C20 C C sing 1.4 N Y
28 C19 N6 C N sing 1.36 N Y
29 C17 C16 C C sing 1.51 N N
30 N4 C12 N C sing 1.35 N N
31 C18 C16 C C doub 1.38 N Y
32 C18 C13 C C sing 1.4 N Y
33 C16 N5 C N sing 1.32 N Y
34 C12 C13 C C sing 1.48 N N
35 C12 O1 C O doub 1.22 N N
36 C13 C14 C C doub 1.4 N Y
37 N5 C15 N C doub 1.32 N Y
38 C14 C15 C C sing 1.38 N Y
39 C1 H1 C H sing 1.09 N N
40 C1 H2 C H sing 1.09 N N
41 C1 H3 C H sing 1.09 N N
42 C2 H4 C H sing 1.09 N N
43 C2 H5 C H sing 1.09 N N
44 C3 H6 C H sing 1.08 N N
45 C14 H8 C H sing 1.08 N N
46 C15 H9 C H sing 1.08 N N
47 C17 H10 C H sing 1.09 N N
48 C17 H11 C H sing 1.09 N N
49 C17 H12 C H sing 1.09 N N
50 C18 H13 C H sing 1.08 N N
51 C20 H14 C H sing 1.08 N N
52 C21 H15 C H sing 1.08 N N
53 C22 H16 C H sing 1.08 N N
54 C24 H17 C H sing 1.09 N N
55 C24 H18 C H sing 1.09 N N
56 C24 H19 C H sing 1.09 N N
57 C26 H20 C H sing 1.09 N N
58 C26 H21 C H sing 1.09 N N
59 C27 H22 C H sing 1.09 N N
60 C27 H23 C H sing 1.09 N N
61 C27 H24 C H sing 1.09 N N
62 C4 H25 C H sing 1.08 N N
63 C10 H28 C H sing 1.09 N N
64 C9 H29 C H sing 1.09 N N
65 C9 H30 C H sing 1.09 N N
66 C8 H31 C H sing 1.09 N N
67 C8 H32 C H sing 1.09 N N
68 C7 H33 C H sing 1.09 N N
69 C6 H34 C H sing 1.09 N N
70 N4 H35 N H sing 0.97 N N
71 C7 H7 C H sing 1.09 N N
72 C6 H26 C H sing 1.09 N N



5XH : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5XH 5feq Open in New Window Bound ligand 1 1
5XH 6q2a Open in New Window Bound ligand 16 1