Chemical Components in the PDB

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92T : Summary

Code

92T

One-letter code

X

Molecule name

1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile

Formula

C24 H17 Cl N8 O

Formal charge

0

Molecular weight

468.898 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Clc1ccccc1n2c(nnc2c3ccncn3)[CH]4C[CH](C4)N5C(=O)Nc6cc(ccc56)C#N
SMILES OpenEye OEToolkits 2.0.6 c1ccc(c(c1)n2c(nnc2C3CC(C3)N4c5ccc(cc5NC4=O)C#N)c6ccncn6)Cl
Canonical SMILES CACTVS 3.385 Clc1ccccc1n2c(nnc2c3ccncn3)[C@@H]4C[C@H](C4)N5C(=O)Nc6cc(ccc56)C#N
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc(c(c1)n2c(nnc2C3CC(C3)N4c5ccc(cc5NC4=O)C#N)c6ccncn6)Cl

IUPAC InChI

InChI=1S/C24H17ClN8O/c25-17-3-1-2-4-20(17)33-22(30-31-23(33)18-7-8-27-13-28-18)15-10-16(11-15)32-21-6-5-14(12-26)9-19(21)29-24(32)34/h1-9,13,15-16H,10-11H2,(H,29,34)/t15-,16-

IUPAC InChI key

MYNRZMIPPXBMLY-WKILWMFISA-N
92T

wwPDB Information

Atom count

51 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-04-12

Last modified at

2017-11-24

Status

Released

Obsoleted

Not Assigned



92T : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N Y N 0 -6.164 -0.88 1.104
2 C4 C C2 N Y N 0 -4.723 0.826 0.544
3 OBD O O1 N N N 0 1.87 -0.582 -2.076
4 CAY C C3 N N N 0 2.866 -0.354 -1.416
5 NAX N N1 N N N 0 3.927 -1.175 -1.306
6 CAW C C4 N Y N 0 4.864 -0.57 -0.47
7 CBC C C5 N Y N 0 6.111 -0.952 -0.011
8 CBB C C6 N Y N 0 6.823 -0.108 0.844
9 CBE C C7 N N N 0 8.115 -0.498 1.323
10 NBF N N2 N N N 0 9.14 -0.807 1.702
11 CBA C C8 N Y N 0 6.274 1.118 1.231
12 CAZ C C9 N Y N 0 5.032 1.496 0.772
13 CAV C C10 N Y N 0 4.32 0.658 -0.078
14 NAU N N3 N N N 0 3.077 0.761 -0.692
15 CAN C C11 N N N 0 2.15 1.887 -0.564
16 CBH C C12 N N N 0 1.178 1.754 0.621
17 CBG C C13 N N N 0 0.921 1.78 -1.482
18 CAH C C14 N N N 0 0.232 1.015 -0.34
19 CAE C C15 N Y N 0 -1.219 1.379 -0.158
20 NAD N N4 N Y N 0 -1.738 2.573 -0.288
21 NAC N N5 N Y N 0 -3.003 2.53 -0.063
22 CAB C C16 N Y N 0 -3.359 1.296 0.224
23 N3 N N6 N Y N 0 -4.95 -0.459 0.819
24 N1 N N7 N Y N 0 -7.198 -0.062 1.126
25 C6 C C17 N Y N 0 -7.055 1.228 0.864
26 C5 C C18 N Y N 0 -5.799 1.721 0.564
27 NAA N N8 N Y N 0 -2.224 0.529 0.163
28 CAG C C19 N Y N 0 -2.123 -0.85 0.39
29 CAI C C20 N Y N 0 -2.267 -1.742 -0.666
30 CL1 CL CL1 N N N 0 -2.571 -1.149 -2.269
31 CAJ C C21 N Y N 0 -2.167 -3.102 -0.438
32 CAK C C22 N Y N 0 -1.924 -3.574 0.839
33 CAL C C23 N Y N 0 -1.781 -2.689 1.891
34 CAM C C24 N Y N 0 -1.875 -1.328 1.669
35 H1 H H1 N N N 0 -6.319 -1.926 1.322
36 H2 H H2 N N N 0 4.023 -2.04 -1.734
37 H3 H H3 N N N 0 6.532 -1.9 -0.311
38 H4 H H4 N N N 0 6.825 1.771 1.892
39 H5 H H5 N N N 0 4.61 2.443 1.073
40 H6 H H6 N N N 0 2.649 2.855 -0.614
41 H7 H H7 N N N 0 1.557 1.128 1.428
42 H8 H H8 N N N 0 0.785 2.708 0.972
43 H9 H H9 N N N 0 0.458 2.742 -1.705
44 H10 H H10 N N N 0 1.093 1.176 -2.373
45 H11 H H11 N N N 0 0.397 -0.062 -0.373
46 H12 H H12 N N N 0 -7.91 1.888 0.885
47 H13 H H13 N N N 0 -5.651 2.769 0.347
48 H14 H H14 N N N 0 -2.278 -3.796 -1.258
49 H15 H H15 N N N 0 -1.846 -4.637 1.014
50 H16 H H16 N N N 0 -1.593 -3.061 2.887
51 H17 H H17 N N N 0 -1.758 -0.638 2.491



92T : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NBF CBE N C trip 1.14 N N
2 CL1 CAI CL C sing 1.74 N N
3 CBE CBB C C sing 1.43 N N
4 CAJ CAI C C doub 1.38 N Y
5 CAJ CAK C C sing 1.38 N Y
6 CBB CBA C C doub 1.4 N Y
7 CBB CBC C C sing 1.4 N Y
8 CBA CAZ C C sing 1.38 N Y
9 CAI CAG C C sing 1.39 N Y
10 CAK CAL C C doub 1.38 N Y
11 CBC CAW C C doub 1.38 N Y
12 CAZ CAV C C doub 1.39 N Y
13 CBH CAH C C sing 1.54 N N
14 CBH CAN C C sing 1.54 N N
15 CAW CAV C C sing 1.4 N Y
16 CAW NAX C N sing 1.39 N N
17 CAV NAU C N sing 1.39 N N
18 CAG NAA C N sing 1.4 N N
19 CAG CAM C C doub 1.39 N Y
20 CAH CAE C C sing 1.51 N N
21 CAH CBG C C sing 1.54 N N
22 CAL CAM C C sing 1.38 N Y
23 C5 C6 C C doub 1.38 N Y
24 C5 C4 C C sing 1.4 N Y
25 NAA CAE N C sing 1.35 N Y
26 NAA CAB N C sing 1.37 N Y
27 NAX CAY N C sing 1.35 N N
28 CAE NAD C N doub 1.31 N Y
29 NAU CAY N C sing 1.35 N N
30 NAU CAN N C sing 1.46 N N
31 C6 N1 C N sing 1.32 N Y
32 CAY OBD C O doub 1.22 N N
33 CAB C4 C C sing 1.48 N N
34 CAB NAC C N doub 1.32 N Y
35 CAN CBG C C sing 1.54 N N
36 NAD NAC N N sing 1.29 N Y
37 C4 N3 C N doub 1.33 N Y
38 N1 C2 N C doub 1.32 N Y
39 N3 C2 N C sing 1.32 N Y
40 C2 H1 C H sing 1.08 N N
41 NAX H2 N H sing 0.97 N N
42 CBC H3 C H sing 1.08 N N
43 CBA H4 C H sing 1.08 N N
44 CAZ H5 C H sing 1.08 N N
45 CAN H6 C H sing 1.09 N N
46 CBH H7 C H sing 1.09 N N
47 CBH H8 C H sing 1.09 N N
48 CBG H9 C H sing 1.09 N N
49 CBG H10 C H sing 1.09 N N
50 CAH H11 C H sing 1.09 N N
51 C6 H12 C H sing 1.08 N N
52 C5 H13 C H sing 1.08 N N
53 CAJ H14 C H sing 1.08 N N
54 CAK H15 C H sing 1.08 N N
55 CAL H16 C H sing 1.08 N N
56 CAM H17 C H sing 1.08 N N



92T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
92T 5nob Open in New Window Bound ligand 2 1