Chemical Components in the PDB

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2F5 : Summary

Code

2F5

One-letter code

X

Molecule name

1H-benzimidazol-2-yl(4-{[3-(morpholin-4-yl)pyrazin-2-yl]oxy}phenyl)methanone

Systematic names

ProgramVersionName
ACDLabs 12.01 1H-benzimidazol-2-yl(4-{[3-(morpholin-4-yl)pyrazin-2-yl]oxy}phenyl)methanone
OpenEye OEToolkits 1.7.6 1H-benzimidazol-2-yl-[4-(3-morpholin-4-ylpyrazin-2-yl)oxyphenyl]methanone

Formula

C22 H19 N5 O3

Formal charge

0

Molecular weight

401.418 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(c2nc1ccccc1n2)c5ccc(Oc4nccnc4N3CCOCC3)cc5
SMILES CACTVS 3.385 O=C(c1[nH]c2ccccc2n1)c3ccc(Oc4nccnc4N5CCOCC5)cc3
SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)[nH]c(n2)C(=O)c3ccc(cc3)Oc4c(nccn4)N5CCOCC5
Canonical SMILES CACTVS 3.385 O=C(c1[nH]c2ccccc2n1)c3ccc(Oc4nccnc4N5CCOCC5)cc3
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)[nH]c(n2)C(=O)c3ccc(cc3)Oc4c(nccn4)N5CCOCC5

IUPAC InChI

InChI=1S/C22H19N5O3/c28-19(20-25-17-3-1-2-4-18(17)26-20)15-5-7-16(8-6-15)30-22-21(23-9-10-24-22)27-11-13-29-14-12-27/h1-10H,11-14H2,(H,25,26)

IUPAC InChI key

YWFDAAMTUBHJGI-UHFFFAOYSA-N
2F5

wwPDB Information

Atom count

49 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-10-07

Last modified at

2013-10-18

Status

Released

Obsoleted

Not Assigned



2F5 : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O01 O O01 N N N 0 3.465 -3.082 0.035
2 C02 C C02 N N N 0 3.152 -1.909 0.106
3 C03 C C03 N Y N 0 4.199 -0.865 0.136
4 N04 N N04 N Y N 0 5.548 -1.102 0.188
5 C05 C C05 N Y N 0 6.173 0.123 0.2
6 C06 C C06 N Y N 0 7.501 0.53 0.246
7 C07 C C07 N Y N 0 7.804 1.874 0.245
8 C08 C C08 N Y N 0 6.793 2.826 0.2
9 C09 C C09 N Y N 0 5.482 2.449 0.156
10 C10 C C10 N Y N 0 5.146 1.088 0.155
11 N11 N N11 N Y N 0 3.977 0.426 0.112
12 C12 C C12 N Y N 0 1.729 -1.527 0.155
13 C13 C C13 N Y N 0 0.741 -2.513 0.248
14 C14 C C14 N Y N 0 -0.586 -2.152 0.294
15 C15 C C15 N Y N 0 -0.946 -0.81 0.249
16 O16 O O16 N N N 0 -2.255 -0.458 0.294
17 C17 C C17 N Y N 0 -2.848 -0.057 -0.859
18 N18 N N18 N Y N 0 -2.132 0.072 -1.963
19 C19 C C19 N Y N 0 -2.714 0.458 -3.088
20 C20 C C20 N Y N 0 -4.067 0.727 -3.115
21 N21 N N21 N Y N 0 -4.793 0.601 -2.015
22 C22 C C22 N Y N 0 -4.221 0.216 -0.885
23 N23 N N23 N N N 0 -4.983 0.077 0.271
24 C24 C C24 N N N 0 -4.44 0.899 1.362
25 C25 C C25 N N N 0 -5.27 0.672 2.628
26 O26 O O26 N N N 0 -6.641 0.973 2.354
27 C27 C C27 N N N 0 -7.202 0.19 1.297
28 C28 C C28 N N N 0 -6.392 0.413 0.018
29 C29 C C29 N Y N 0 0.033 0.174 0.156
30 C30 C C30 N Y N 0 1.363 -0.177 0.115
31 H1 H H1 N N N 0 5.98 -1.97 0.21
32 H2 H H2 N N N 0 8.292 -0.205 0.281
33 H3 H H3 N N N 0 8.836 2.19 0.281
34 H4 H H4 N N N 0 7.047 3.875 0.201
35 H5 H H5 N N N 0 4.705 3.198 0.121
36 H7 H H7 N N N 0 1.02 -3.556 0.283
37 H8 H H8 N N N 0 -1.349 -2.913 0.366
38 H9 H H9 N N N 0 -2.127 0.564 -3.989
39 H10 H H10 N N N 0 -4.534 1.042 -4.036
40 H11 H H11 N N N 0 -3.404 0.616 1.55
41 H12 H H12 N N N 0 -4.485 1.952 1.082
42 H13 H H13 N N N 0 -5.181 -0.37 2.939
43 H14 H H14 N N N 0 -4.906 1.322 3.424
44 H15 H H15 N N N 0 -7.17 -0.865 1.569
45 H16 H H16 N N N 0 -8.236 0.491 1.131
46 H17 H H17 N N N 0 -6.468 1.457 -0.284
47 H18 H H18 N N N 0 -6.781 -0.225 -0.776
48 H19 H H19 N N N 0 -0.25 1.216 0.121
49 H20 H H20 N N N 0 2.123 0.587 0.048



2F5 : 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 C19 C20 C C doub 1.379746 N Y
2 C19 N18 C N sing 1.3241394 N Y
3 C20 N21 C N sing 1.323991 N Y
4 O01 C02 O C doub 1.2161163 N N
5 N18 C17 N C doub 1.3221623 N Y
6 N21 C22 N C doub 1.3237481 N Y
7 C02 C03 C C sing 1.4788661 N N
8 C02 C12 C C sing 1.4741961 N N
9 C03 N11 C N doub 1.3101683 N Y
10 C03 N04 C N sing 1.3706473 N Y
11 C30 C12 C C doub 1.3993056 N Y
12 C30 C29 C C sing 1.3761475 N Y
13 N11 C10 N C sing 1.3441184 N Y
14 N04 C05 N C sing 1.3752797 N Y
15 C12 C13 C C sing 1.3989242 N Y
16 C10 C05 C C doub 1.409957 N Y
17 C10 C09 C C sing 1.4018624 N Y
18 C05 C06 C C sing 1.3897299 N Y
19 C29 C15 C C doub 1.3911672 N Y
20 C17 C22 C C sing 1.4001193 N Y
21 C17 O16 C O sing 1.357151 N N
22 C09 C08 C C doub 1.3648392 N Y
23 C06 C07 C C doub 1.3777322 N Y
24 C22 N23 C N sing 1.3915104 N N
25 C08 C07 C C sing 1.3894063 N Y
26 C13 C14 C C doub 1.3759964 N Y
27 C15 C14 C C sing 1.3901759 N Y
28 C15 O16 C O sing 1.3562485 N N
29 N23 C28 N C sing 1.4704374 N N
30 N23 C24 N C sing 1.4699707 N N
31 C28 C27 C C sing 1.5302516 N N
32 C24 C25 C C sing 1.5307466 N N
33 C27 O26 C O sing 1.4300556 N N
34 C25 O26 C O sing 1.4301461 N N
35 N04 H1 N H sing 0.9698103 N N
36 C06 H2 C H sing 1.0803384 N N
37 C07 H3 C H sing 1.0798963 N N
38 C08 H4 C H sing 1.0793136 N N
39 C09 H5 C H sing 1.0797939 N N
40 C13 H7 C H sing 1.0802383 N N
41 C14 H8 C H sing 1.0800343 N N
42 C19 H9 C H sing 1.0805582 N N
43 C20 H10 C H sing 1.0796087 N N
44 C24 H11 C H sing 1.0902885 N N
45 C24 H12 C H sing 1.09052 N N
46 C25 H13 C H sing 1.0910573 N N
47 C25 H14 C H sing 1.0902349 N N
48 C27 H15 C H sing 1.0899693 N N
49 C27 H16 C H sing 1.089639 N N
50 C28 H17 C H sing 1.0894568 N N
51 C28 H18 C H sing 1.0903215 N N
52 C29 H19 C H sing 1.0803138 N N
53 C30 H20 C H sing 1.0797153 N N



2F5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2F5 4mvh Open in New Window Bound ligand 2 1