Chemical Components in the PDB

pdbe.org/chem
spacer

T3C : Summary

Code

T3C

One-letter code

X

Molecule name

2-[[3-(1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile

Systematic names

ProgramVersionName
ACDLabs 12.01 2-{[3-(1,4-diazepan-1-yl)phenyl]amino}-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile
OpenEye OEToolkits 1.9.2 2-[[3-(1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile

Formula

C21 H24 N8 S

Formal charge

0

Molecular weight

420.534 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N#Cc1c(nc(nc1)Nc3cccc(N2CCCNCC2)c3)c4sc(nc4C)NC
SMILES CACTVS 3.385 CNc1sc(c(C)n1)c2nc(Nc3cccc(c3)N4CCCNCC4)ncc2C#N
SMILES OpenEye OEToolkits 1.9.2 Cc1c(sc(n1)NC)c2c(cnc(n2)Nc3cccc(c3)N4CCCNCC4)C#N
Canonical SMILES CACTVS 3.385 CNc1sc(c(C)n1)c2nc(Nc3cccc(c3)N4CCCNCC4)ncc2C#N
Canonical SMILES OpenEye OEToolkits 1.9.2 Cc1c(sc(n1)NC)c2c(cnc(n2)Nc3cccc(c3)N4CCCNCC4)C#N

IUPAC InChI

InChI=1S/C21H24N8S/c1-14-19(30-21(23-2)26-14)18-15(12-22)13-25-20(28-18)27-16-5-3-6-17(11-16)29-9-4-7-24-8-10-29/h3,5-6,11,13,24H,4,7-10H2,1-2H3,(H,23,26)(H,25,27,28)

IUPAC InChI key

BKOYUSKBPMSUBK-UHFFFAOYSA-N
T3C

wwPDB Information

Atom count

54 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-10-02

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



T3C : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 8.371 -0.105 1.147
2 C03 C C03 N Y N 0 6.066 0.337 0.393
3 C05 C C05 N Y N 0 4.333 -1.039 0.658
4 C06 C C06 N N N 0 3.668 -2.31 1.121
5 C07 C C07 N Y N 0 3.663 -0.051 0.02
6 C08 C C08 N Y N 0 2.232 -0.052 -0.314
7 C10 C C10 N Y N 0 0.17 -1.09 -0.29
8 C12 C C12 N Y N 0 -1.981 -2.162 -0.137
9 C13 C C13 N Y N 0 -2.654 -3.331 -0.47
10 C14 C C14 N Y N 0 -4.021 -3.31 -0.669
11 C15 C C15 N Y N 0 -4.723 -2.128 -0.538
12 C16 C C16 N Y N 0 -4.056 -0.955 -0.206
13 C18 C C18 N N N 0 -6.132 0.042 -0.315
14 C19 C C19 N N N 0 -6.898 1.383 -0.372
15 C20 C C20 N N N 0 -7.077 1.904 1.031
16 C22 C C22 N N N 0 -4.647 2.384 1.034
17 C23 C C23 N N N 0 -4.46 0.899 1.213
18 C24 C C24 N Y N 0 -2.684 -0.974 0.0010
19 C26 C C26 N Y N 0 0.279 0.993 -1.278
20 C27 C C27 N Y N 0 1.645 1.052 -0.982
21 C28 C C28 N N N 0 2.429 2.193 -1.348
22 H011 H H011 N N N 0 8.071 -0.29 2.179
23 H012 H H012 N N N 0 8.438 -1.052 0.613
24 H013 H H013 N N N 0 9.343 0.389 1.135
25 H02 H H02 N N N 0 7.643 1.616 0.139
26 H061 H H061 N N N 0 3.297 -2.176 2.138
27 H062 H H062 N N N 0 2.836 -2.547 0.459
28 H063 H H063 N N N 0 4.391 -3.125 1.103
29 H11 H H11 N N N 0 -0.176 -2.967 0.452
30 H13 H H13 N N N 0 -2.108 -4.257 -0.573
31 H14 H H14 N N N 0 -4.542 -4.22 -0.928
32 H15 H H15 N N N 0 -5.792 -2.115 -0.694
33 H181 H H181 N N N 0 -6.254 -0.478 -1.265
34 H182 H H182 N N N 0 -6.549 -0.573 0.482
35 H191 H H191 N N N 0 -6.329 2.103 -0.959
36 H192 H H192 N N N 0 -7.874 1.226 -0.83
37 H201 H H201 N N N 0 -8.029 2.431 1.091
38 H202 H H202 N N N 0 -7.103 1.059 1.719
39 H21 H H21 N N N 0 -6.18 3.765 1.134
40 H221 H H221 N N N 0 -4.497 2.637 -0.015
41 H222 H H222 N N N 0 -3.903 2.91 1.634
42 H231 H H231 N N N 0 -5.137 0.533 1.984
43 H232 H H232 N N N 0 -3.429 0.689 1.497
44 H24 H H24 N N N 0 -2.164 -0.065 0.264
45 H26 H H26 N N N 0 -0.206 1.811 -1.79
46 N02 N N02 N N N 0 7.379 0.754 0.497
47 N04 N N04 N Y N 0 5.609 -0.796 0.838
48 N09 N N09 N Y N 0 1.459 -1.088 0.01
49 N11 N N11 N N N 0 -0.598 -2.184 0.064
50 N17 N N17 N N N 0 -4.767 0.24 -0.073
51 N21 N N21 N N N 0 -5.995 2.824 1.448
52 N25 N N25 N Y N 0 -0.41 -0.075 -0.919
53 N29 N N29 N N N 0 3.051 3.099 -1.638
54 S30 S S30 N Y N 0 4.809 1.24 -0.333



T3C : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 N02 C N sing 1.4643924 N N
2 N02 C03 N C sing 1.3815477 N N
3 C03 N04 C N doub 1.3002166 N Y
4 C03 S30 C S sing 1.709542 N Y
5 N04 C05 N C sing 1.3113447 N Y
6 C05 C06 C C sing 1.5073271 N N
7 C05 C07 C C doub 1.3535465 N Y
8 C07 C08 C C sing 1.4694618 N N
9 C07 S30 C S sing 1.7619892 N Y
10 C08 N09 C N sing 1.3325919 N Y
11 C08 C27 C C doub 1.4176068 N Y
12 N09 C10 N C doub 1.3234519 N Y
13 C10 N11 C N sing 1.3827422 N N
14 C10 N25 C N sing 1.3275037 N Y
15 N11 C12 N C sing 1.3977032 N N
16 C12 C13 C C sing 1.3893808 N Y
17 C12 C24 C C doub 1.3872985 N Y
18 C13 C14 C C doub 1.3815683 N Y
19 C14 C15 C C sing 1.3809739 N Y
20 C15 C16 C C doub 1.3896194 N Y
21 C16 N17 C N sing 1.3968661 N N
22 C16 C24 C C sing 1.3876578 N Y
23 N17 C18 N C sing 1.4003546 N N
24 N17 C23 N C sing 1.4772698 N N
25 C18 C19 C C sing 1.545408 N N
26 C19 C20 C C sing 1.5072794 N N
27 C20 N21 C N sing 1.4802071 N N
28 N21 C22 N C sing 1.4771932 N N
29 C22 C23 C C sing 1.5073935 N N
30 N25 C26 N C doub 1.3206915 N Y
31 C26 C27 C C sing 1.3989471 N Y
32 C27 C28 C C sing 1.4319543 N N
33 C28 N29 C N trip 1.1365826 N N
34 C01 H011 C H sing 1.0905269 N N
35 C01 H012 C H sing 1.0892447 N N
36 C01 H013 C H sing 1.0903963 N N
37 N02 H02 N H sing 0.97000206 N N
38 C06 H061 C H sing 1.090819 N N
39 C06 H062 C H sing 1.0893286 N N
40 C06 H063 C H sing 1.0896229 N N
41 N11 H11 N H sing 0.970421 N N
42 C13 H13 C H sing 1.0799079 N N
43 C24 H24 C H sing 1.0797453 N N
44 C14 H14 C H sing 1.0801028 N N
45 C15 H15 C H sing 1.0804008 N N
46 C18 H181 C H sing 1.0898551 N N
47 C18 H182 C H sing 1.0896435 N N
48 C23 H231 C H sing 1.0893695 N N
49 C23 H232 C H sing 1.0898243 N N
50 C19 H191 C H sing 1.0893713 N N
51 C19 H192 C H sing 1.0894903 N N
52 C20 H201 C H sing 1.0897858 N N
53 C20 H202 C H sing 1.0899748 N N
54 N21 H21 N H sing 1.0091095 N N
55 C22 H221 C H sing 1.0894539 N N
56 C22 H222 C H sing 1.0909684 N N
57 C26 H26 C H sing 1.0800431 N N



T3C : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
T3C 4bcg Open in New Window Bound ligand 1 1
T3C 4bcp Open in New Window Bound ligand 2 1