Chemical Components in the PDB

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STI : Summary

Code

STI

One-letter code

X

Molecule name

4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 4-[(4-methylpiperazin-1-yl)methyl]-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide
OpenEye OEToolkits 1.5.0 4-[(4-methylpiperazin-1-yl)methyl]-N-[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide

Formula

C29 H31 N7 O

Formal charge

0

Molecular weight

493.603 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(Nc3ccc(c(Nc2nc(c1cccnc1)ccn2)c3)C)c4ccc(cc4)CN5CCN(CC5)C
SMILES CACTVS 3.341 CN1CCN(CC1)Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3
SMILES OpenEye OEToolkits 1.5.0 Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C
Canonical SMILES CACTVS 3.341 CN1CCN(CC1)Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C

IUPAC InChI

InChI=1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)

IUPAC InChI key

KTUFNOKKBVMGRW-UHFFFAOYSA-N
STI

wwPDB Information

Atom count

68 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-04-11

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



STI : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 2.74 -0.022 8.889
2 C6 C C6 N Y N 0 1.914 0.207 7.802
3 C5 C C5 N Y N 0 2.435 0.009 6.52
4 C4 C C4 N Y N 0 3.755 -0.413 6.387
5 N3 N N3 N Y N 0 4.505 -0.614 7.452
6 C2 C C2 N Y N 0 4.042 -0.436 8.674
7 C7 C C7 N Y N 0 1.593 0.241 5.321
8 C12 C C12 N Y N 0 2.131 0.848 4.183
9 C11 C C11 N Y N 0 1.308 1.042 3.088
10 N10 N N10 N Y N 0 0.045 0.651 3.15
11 C9 C C9 N Y N 0 -0.438 0.077 4.242
12 N8 N N8 N Y N 0 0.313 -0.122 5.314
13 N13 N N13 N N N 0 -1.765 -0.317 4.266
14 C14 C C14 N Y N 0 -2.541 -0.23 3.106
15 C19 C C19 N Y N 0 -3.901 0.04 3.198
16 C18 C C18 N Y N 0 -4.669 0.126 2.052
17 C17 C C17 N Y N 0 -4.087 -0.056 0.812
18 C16 C C16 N Y N 0 -2.728 -0.327 0.714
19 C15 C C15 N Y N 0 -1.955 -0.419 1.862
20 N21 N N21 N N N 0 -2.14 -0.512 -0.541
21 C22 C C22 N N N 0 -2.547 0.228 -1.591
22 C23 C C23 N Y N 0 -1.994 -0.031 -2.937
23 C25 C C25 N Y N 0 -2.413 0.734 -4.027
24 C26 C C26 N Y N 0 -1.892 0.486 -5.28
25 C27 C C27 N Y N 0 -0.957 -0.517 -5.458
26 C28 C C28 N Y N 0 -0.542 -1.283 -4.384
27 C29 C C29 N Y N 0 -1.05 -1.042 -3.124
28 C46 C C46 N N N 0 -0.393 -0.781 -6.83
29 N48 N N48 N N N 0 0.809 0.038 -7.032
30 C53 C C53 N N N 0 1.306 -0.264 -8.379
31 C52 C C52 N N N 0 2.629 0.463 -8.615
32 N51 N N51 N N N 0 3.638 -0.027 -7.668
33 C54 C C54 N N N 0 4.84 0.792 -7.87
34 C50 C C50 N N N 0 3.141 0.276 -6.321
35 C49 C C49 N N N 0 1.817 -0.452 -6.085
36 O29 O O29 N N N 0 -3.368 1.11 -1.431
37 C20 C C20 N N N 0 -4.539 0.24 4.548
38 H11 H 1H1 N N N 0 2.371 0.12 9.894
39 H61 H 1H6 N N N 0 0.893 0.532 7.941
40 H41 H 1H4 N N N 0 4.171 -0.57 5.403
41 H21 H 1H2 N N N 0 4.689 -0.616 9.519
42 H121 H 1H12 N N N 0 3.166 1.157 4.159
43 H111 H 1H11 N N N 0 1.692 1.508 2.193
44 H131 H 1H13 N N N 0 -2.157 -0.654 5.087
45 H181 H 1H18 N N N 0 -5.725 0.336 2.126
46 H171 H 1H17 N N N 0 -4.69 0.011 -0.08
47 H151 H 1H15 N N N 0 -0.899 -0.63 1.788
48 H211 H 1H21 N N N 0 -1.44 -1.173 -0.656
49 H251 H 1H25 N N N 0 -3.142 1.518 -3.889
50 H261 H 1H26 N N N 0 -2.216 1.077 -6.124
51 H281 H 1H28 N N N 0 0.187 -2.065 -4.53
52 H291 H 1H29 N N N 0 -0.722 -1.638 -2.285
53 H461 H 1H46 N N N 0 -1.137 -0.526 -7.585
54 H462 H 2H46 N N N 0 -0.132 -1.836 -6.919
55 H531 H 1H53 N N N 0 0.574 0.063 -9.118
56 H532 H 2H53 N N N 0 1.46 -1.339 -8.475
57 H521 H 1H52 N N N 0 2.486 1.533 -8.47
58 H522 H 2H52 N N N 0 2.968 0.278 -9.635
59 H541 H 1H54 N N N 0 5.623 0.464 -7.185
60 H542 H 2H54 N N N 0 5.187 0.682 -8.897
61 H543 H 3H54 N N N 0 4.603 1.838 -7.676
62 H501 H 1H50 N N N 0 3.872 -0.052 -5.582
63 H502 H 2H50 N N N 0 2.986 1.35 -6.225
64 H491 H 1H49 N N N 0 1.478 -0.267 -5.065
65 H492 H 2H49 N N N 0 1.961 -1.522 -6.23
66 H201 H 1H20 N N N 0 -4.89 -0.718 4.93
67 H202 H 2H20 N N N 0 -3.807 0.661 5.237
68 H203 H 3H20 N N N 0 -5.383 0.924 4.453



STI : 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 C6 C C doub 1.38 N Y
2 C1 C2 C C sing 1.38 N Y
3 C1 H11 C H sing 1.08 N N
4 C6 C5 C C sing 1.4 N Y
5 C6 H61 C H sing 1.08 N N
6 C5 C4 C C doub 1.39 N Y
7 C5 C7 C C sing 1.48 N Y
8 C4 N3 C N sing 1.32 N Y
9 C4 H41 C H sing 1.08 N N
10 N3 C2 N C doub 1.32 N Y
11 C2 H21 C H sing 1.08 N N
12 C7 C12 C C doub 1.4 N Y
13 C7 N8 C N sing 1.33 N Y
14 C12 C11 C C sing 1.38 N Y
15 C12 H121 C H sing 1.08 N N
16 C11 N10 C N doub 1.32 N Y
17 C11 H111 C H sing 1.08 N N
18 N10 C9 N C sing 1.32 N Y
19 C9 N8 C N doub 1.32 N Y
20 C9 N13 C N sing 1.38 N N
21 N13 C14 N C sing 1.4 N N
22 N13 H131 N H sing 0.97 N N
23 C14 C19 C C doub 1.39 N Y
24 C14 C15 C C sing 1.39 N Y
25 C19 C18 C C sing 1.38 N Y
26 C19 C20 C C sing 1.51 N N
27 C18 C17 C C doub 1.38 N Y
28 C18 H181 C H sing 1.08 N N
29 C17 C16 C C sing 1.39 N Y
30 C17 H171 C H sing 1.08 N N
31 C16 C15 C C doub 1.39 N Y
32 C16 N21 C N sing 1.4 N N
33 C15 H151 C H sing 1.08 N N
34 N21 C22 N C sing 1.35 N N
35 N21 H211 N H sing 0.97 N N
36 C22 C23 C C sing 1.48 N N
37 C22 O29 C O doub 1.22 N N
38 C23 C25 C C doub 1.4 N Y
39 C23 C29 C C sing 1.4 N Y
40 C25 C26 C C sing 1.38 N Y
41 C25 H251 C H sing 1.08 N N
42 C26 C27 C C doub 1.38 N Y
43 C26 H261 C H sing 1.08 N N
44 C27 C28 C C sing 1.38 N Y
45 C27 C46 C C sing 1.51 N N
46 C28 C29 C C doub 1.38 N Y
47 C28 H281 C H sing 1.08 N N
48 C29 H291 C H sing 1.08 N N
49 C46 N48 C N sing 1.47 N N
50 C46 H461 C H sing 1.09 N N
51 C46 H462 C H sing 1.09 N N
52 N48 C53 N C sing 1.47 N N
53 N48 C49 N C sing 1.47 N N
54 C53 C52 C C sing 1.53 N N
55 C53 H531 C H sing 1.09 N N
56 C53 H532 C H sing 1.09 N N
57 C52 N51 C N sing 1.47 N N
58 C52 H521 C H sing 1.09 N N
59 C52 H522 C H sing 1.09 N N
60 N51 C54 N C sing 1.47 N N
61 N51 C50 N C sing 1.47 N N
62 C54 H541 C H sing 1.09 N N
63 C54 H542 C H sing 1.09 N N
64 C54 H543 C H sing 1.09 N N
65 C50 C49 C C sing 1.53 N N
66 C50 H501 C H sing 1.09 N N
67 C50 H502 C H sing 1.09 N N
68 C49 H491 C H sing 1.09 N N
69 C49 H492 C H sing 1.09 N N
70 C20 H201 C H sing 1.09 N N
71 C20 H202 C H sing 1.09 N N
72 C20 H203 C H sing 1.09 N N



STI : Used in PDB Entries

Total Number of PDB Entries: 28
Ligand Code PDB Entry ID Type Total Distinct
STI 1iep Open in New Window Bound ligand 2 1
STI 1opj Open in New Window Bound ligand 2 1
STI 1t46 Open in New Window Bound ligand 1 1
STI 1xbb Open in New Window Bound ligand 1 1
STI 2hyy Open in New Window Bound ligand 4 1
STI 2oiq Open in New Window Bound ligand 1 1
STI 2pl0 Open in New Window Bound ligand 1 1
STI 3fw1 Open in New Window Bound ligand 1 1
STI 3gvu Open in New Window Bound ligand 2 1
STI 3hec Open in New Window Bound ligand 1 1
STI 3k5v Open in New Window Bound ligand 2 1
STI 3ms9 Open in New Window Bound ligand 2 1
STI 3mss Open in New Window Bound ligand 4 1
STI 3oez Open in New Window Bound ligand 2 1
STI 3pyy Open in New Window Bound ligand 2 1
STI 4bkj Open in New Window Bound ligand 2 1
STI 4csv Open in New Window Bound ligand 1 1
STI 4r7i Open in New Window Bound ligand 1 1
STI 5mqt Open in New Window Bound ligand 2 1
STI 6hd4 Open in New Window Bound ligand 2 1
STI 6hd6 Open in New Window Bound ligand 2 1
STI 6jol Open in New Window Bound ligand 1 1
STI 6ktn Open in New Window Bound ligand 1 1
STI 6npe Open in New Window Bound ligand 2 1
STI 6npu Open in New Window Bound ligand 2 1
STI 6npv Open in New Window Bound ligand 2 1
STI 6vxh Open in New Window Bound ligand 1 1
STI 7n9g Open in New Window Bound ligand 3 1