Chemical Components in the PDB

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IBI : Summary

Code

IBI

One-letter code

X

Molecule name

N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide

Synonyms

Volasertib

Systematic names

ProgramVersionName
ACDLabs 10.04 N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide
OpenEye OEToolkits 1.5.0 N-[4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl]-4-[[(7R)-7-ethyl-5-methyl-6-oxo-8-propan-2-yl-7H-pteridin-2-yl]amino]-3-methoxy-benzamide

Formula

C34 H50 N8 O3

Formal charge

0

Molecular weight

618.813 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C6N(c1c(nc(nc1)Nc2ccc(cc2OC)C(=O)NC5CCC(N3CCN(CC3)CC4CC4)CC5)N(C(C)C)C6CC)C
SMILES CACTVS 3.341 CC[CH]1N(C(C)C)c2nc(Nc3ccc(cc3OC)C(=O)N[CH]4CC[CH](CC4)N5CCN(CC5)CC6CC6)ncc2N(C)C1=O
SMILES OpenEye OEToolkits 1.5.0 CCC1C(=O)N(c2cnc(nc2N1C(C)C)Nc3ccc(cc3OC)C(=O)NC4CCC(CC4)N5CCN(CC5)CC6CC6)C
Canonical SMILES CACTVS 3.341 CC[C@H]1N(C(C)C)c2nc(Nc3ccc(cc3OC)C(=O)N[C@H]4CC[C@@H](CC4)N5CCN(CC5)CC6CC6)ncc2N(C)C1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC[C@@H]1C(=O)N(c2cnc(nc2N1C(C)C)Nc3ccc(cc3OC)C(=O)NC4CCC(CC4)N5CCN(CC5)CC6CC6)C

IUPAC InChI

InChI=1S/C34H50N8O3/c1-6-28-33(44)39(4)29-20-35-34(38-31(29)42(28)22(2)3)37-27-14-9-24(19-30(27)45-5)32(43)36-25-10-12-26(13-11-25)41-17-15-40(16-18-41)21-23-7-8-23/h9,14,19-20,22-23,25-26,28H,6-8,10-13,15-18,21H2,1-5H3,(H,36,43)(H,35,37,38)/t25-,26-,28-/m1/s1

IUPAC InChI key

SXNJFOWDRLKDSF-STROYTFGSA-N
IBI

wwPDB Information

Atom count

95 (45 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-11-25

Last modified at

2018-03-29

Status

Released

Obsoleted

Not Assigned



IBI : Atoms of Molecule

Total Number of Atoms: 95
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 -8.109 2.109 -0.788
2 C2 C C2 N N N 0 -9.623 2.307 -0.689
3 C5 C C5 N N N 0 -8.249 0.257 0.764
4 C6 C C6 N N N 0 -9.763 0.455 0.863
5 C7 C C7 N N N 0 -4.126 0.804 1.786
6 C8 C C8 N N N 0 -5.649 0.944 1.815
7 C11 C C11 N N N 0 -4.223 0.249 -0.648
8 C12 C C12 N N N 0 -5.747 0.389 -0.619
9 C15 C C15 N Y N 0 0.571 -0.575 0.655
10 C16 C C16 N Y N 0 1.724 -2.93 -0.275
11 C17 C C17 N Y N 0 -0.236 -1.627 0.216
12 C18 C C18 N Y N 0 0.35 -2.808 -0.251
13 C21 C C21 R N N 0 8.911 0.819 -0.934
14 N22 N N22 N N N 0 7.035 2.407 -0.704
15 C24 C C24 N Y N 0 6.225 1.286 -0.473
16 C31 C C31 N N N 0 10.392 0.836 -0.552
17 C32 C C32 N N N 0 10.971 -0.573 -0.691
18 C33 C C33 N N N 0 8.586 0.197 1.38
19 C34 C C34 N N N 0 8.052 1.558 1.83
20 C35 C C35 N N N 0 8.015 -0.899 2.283
21 C36 C C36 N N N 0 6.453 3.751 -0.764
22 C38 C C38 N N N 0 1.416 -5.115 -1.162
23 C39 C C39 N N N 0 -1.706 -1.492 0.244
24 O40 O O40 N N N 0 -2.408 -2.408 -0.139
25 O37 O O37 N N N 0 2.297 -4.077 -0.727
26 C14 C C14 N Y N 0 2.526 -1.875 0.166
27 N19 N N19 N N N 0 3.915 -1.999 0.141
28 C26 C C26 N Y N 0 4.707 -0.879 -0.062
29 N27 N N27 N Y N 0 6.024 -0.998 0.035
30 C25 C C25 N Y N 0 6.81 0.056 -0.154
31 N23 N N23 N N N 0 8.182 -0.054 -0.0090
32 N28 N N28 N Y N 0 4.126 0.276 -0.346
33 C29 C C29 N Y N 0 4.847 1.37 -0.557
34 C20 C C20 N N N 0 8.363 2.221 -0.871
35 O30 O O30 N N N 0 9.107 3.174 -0.967
36 C13 C C13 N Y N 0 1.943 -0.702 0.629
37 N41 N N41 N N N 0 -2.269 -0.354 0.694
38 C9 C C9 N N N 0 -3.728 -0.22 0.722
39 C10 C C10 N N N 0 -6.145 1.413 0.446
40 N3 N N3 N N N 0 -7.607 1.547 0.474
41 N4 N N4 N N N 0 -10.265 1.017 -0.399
42 C42 C C42 N N N 0 -11.727 1.151 -0.371
43 C43 C C43 N N N 0 -12.366 -0.238 -0.316
44 C45 C C45 N N N 0 -13.887 -0.311 -0.162
45 C44 C C44 N N N 0 -13.235 -0.664 -1.501
46 H1 H H1 N N N 0 -7.884 1.424 -1.606
47 H1A H H1A N N N 0 -7.628 3.069 -0.975
48 H2 H H2 N N N 0 -9.847 3.012 0.111
49 H2A H H2A N N N 0 -10.002 2.696 -1.634
50 H5 H H5 N N N 0 -7.871 -0.133 1.709
51 H5A H H5A N N N 0 -8.026 -0.448 -0.036
52 H6 H H6 N N N 0 -10.244 -0.506 1.05
53 H6A H H6A N N N 0 -9.988 1.139 1.681
54 H7 H H7 N N N 0 -3.677 1.768 1.548
55 H7A H H7A N N N 0 -3.773 0.47 2.762
56 H8 H H8 N N N 0 -6.098 -0.021 2.053
57 H8A H H8A N N N 0 -5.933 1.673 2.574
58 H11 H H11 N N N 0 -3.94 -0.481 -1.406
59 H11A H H11A N N N 0 -3.775 1.213 -0.886
60 H12 H H12 N N N 0 -6.1 0.723 -1.594
61 H12A H H12A N N N 0 -6.195 -0.576 -0.381
62 H15 H H15 N N N 0 0.12 0.339 1.012
63 H18 H H18 N N N 0 -0.272 -3.623 -0.591
64 H21 H H21 N N N 0 8.804 0.438 -1.95
65 H31 H H31 N N N 0 10.93 1.516 -1.213
66 H31A H H31A N N N 0 10.498 1.173 0.479
67 H32 H H32 N N N 0 12.002 -0.579 -0.336
68 H32A H H32A N N N 0 10.379 -1.269 -0.097
69 H32B H H32B N N N 0 10.945 -0.876 -1.738
70 H33 H H33 N N N 0 9.674 0.193 1.448
71 H34 H H34 N N N 0 8.352 1.744 2.861
72 H34A H H34A N N N 0 8.458 2.339 1.187
73 H34B H H34B N N N 0 6.964 1.561 1.762
74 H35 H H35 N N N 0 6.932 -0.933 2.171
75 H35A H H35A N N N 0 8.441 -1.861 2.0
76 H35B H H35B N N N 0 8.267 -0.682 3.321
77 H36 H H36 N N N 0 6.451 4.19 0.233
78 H36A H H36A N N N 0 7.046 4.373 -1.435
79 H36B H H36B N N N 0 5.431 3.688 -1.136
80 H38 H H38 N N N 0 2.001 -5.972 -1.497
81 H38A H H38A N N N 0 0.773 -5.415 -0.335
82 H38B H H38B N N N 0 0.803 -4.749 -1.986
83 HN19 H HN19 N N N 0 4.326 -2.869 0.265
84 H29 H H29 N N N 0 4.367 2.309 -0.79
85 H13 H H13 N N N 0 2.566 0.112 0.969
86 HN41 H HN41 N N N 0 -1.709 0.377 0.999
87 H9 H H9 N N N 0 -4.177 -1.185 0.96
88 H10 H H10 N N N 0 -5.696 2.377 0.208
89 H42 H H42 N N N 0 -12.023 1.722 0.509
90 H42A H H42A N N N 0 -12.062 1.669 -1.27
91 H43 H H43 N N N 0 -11.773 -1.009 0.176
92 H45 H H45 N N N 0 -14.294 -1.13 0.43
93 H45A H H45A N N N 0 -14.432 0.63 -0.1
94 H44 H H44 N N N 0 -13.352 0.046 -2.32
95 H44A H H44A N N N 0 -13.214 -1.715 -1.789



IBI : Chemical Bonds

Total Number of Bonds: 100
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 N3 C N sing 1.47 N N
3 C2 N4 C N sing 1.47 N N
4 C5 C6 C C sing 1.53 N N
5 C5 N3 C N sing 1.47 N N
6 C6 N4 C N sing 1.47 N N
7 C7 C8 C C sing 1.53 N N
8 C7 C9 C C sing 1.53 N N
9 C8 C10 C C sing 1.53 N N
10 C11 C12 C C sing 1.53 N N
11 C11 C9 C C sing 1.53 N N
12 C12 C10 C C sing 1.53 N N
13 C15 C17 C C doub 1.4 N Y
14 C15 C13 C C sing 1.38 N Y
15 C16 C18 C C doub 1.38 N Y
16 C16 O37 C O sing 1.36 N N
17 C16 C14 C C sing 1.4 N Y
18 C17 C18 C C sing 1.4 N Y
19 C17 C39 C C sing 1.48 N N
20 C21 C31 C C sing 1.53 N N
21 C21 N23 C N sing 1.47 N N
22 C21 C20 C C sing 1.51 N N
23 N22 C24 N C sing 1.4 N N
24 N22 C36 N C sing 1.47 N N
25 N22 C20 N C sing 1.35 N N
26 C24 C25 C C doub 1.4 N Y
27 C24 C29 C C sing 1.38 N Y
28 C31 C32 C C sing 1.53 N N
29 C33 C34 C C sing 1.53 N N
30 C33 C35 C C sing 1.53 N N
31 C33 N23 C N sing 1.47 N N
32 C38 O37 C O sing 1.43 N N
33 C39 O40 C O doub 1.22 N N
34 C39 N41 C N sing 1.35 N N
35 C14 N19 C N sing 1.39 N N
36 C14 C13 C C doub 1.39 N Y
37 N19 C26 N C sing 1.39 N N
38 C26 N27 C N doub 1.33 N Y
39 C26 N28 C N sing 1.32 N Y
40 N27 C25 N C sing 1.33 N Y
41 C25 N23 C N sing 1.38 N N
42 N28 C29 N C doub 1.33 N Y
43 C20 O30 C O doub 1.21 N N
44 N41 C9 N C sing 1.47 N N
45 C10 N3 C N sing 1.47 N N
46 N4 C42 N C sing 1.47 N N
47 C42 C43 C C sing 1.53 N N
48 C43 C45 C C sing 1.53 N N
49 C43 C44 C C sing 1.53 N N
50 C45 C44 C C sing 1.53 N N
51 C1 H1 C H sing 1.09 N N
52 C1 H1A C H sing 1.09 N N
53 C2 H2 C H sing 1.09 N N
54 C2 H2A C H sing 1.09 N N
55 C5 H5 C H sing 1.09 N N
56 C5 H5A C H sing 1.09 N N
57 C6 H6 C H sing 1.09 N N
58 C6 H6A C H sing 1.09 N N
59 C7 H7 C H sing 1.09 N N
60 C7 H7A C H sing 1.09 N N
61 C8 H8 C H sing 1.09 N N
62 C8 H8A C H sing 1.09 N N
63 C11 H11 C H sing 1.09 N N
64 C11 H11A C H sing 1.09 N N
65 C12 H12 C H sing 1.09 N N
66 C12 H12A C H sing 1.09 N N
67 C15 H15 C H sing 1.08 N N
68 C18 H18 C H sing 1.08 N N
69 C21 H21 C H sing 1.09 N N
70 C31 H31 C H sing 1.09 N N
71 C31 H31A C H sing 1.09 N N
72 C32 H32 C H sing 1.09 N N
73 C32 H32A C H sing 1.09 N N
74 C32 H32B C H sing 1.09 N N
75 C33 H33 C H sing 1.09 N N
76 C34 H34 C H sing 1.09 N N
77 C34 H34A C H sing 1.09 N N
78 C34 H34B C H sing 1.09 N N
79 C35 H35 C H sing 1.09 N N
80 C35 H35A C H sing 1.09 N N
81 C35 H35B C H sing 1.09 N N
82 C36 H36 C H sing 1.09 N N
83 C36 H36A C H sing 1.09 N N
84 C36 H36B C H sing 1.09 N N
85 C38 H38 C H sing 1.09 N N
86 C38 H38A C H sing 1.09 N N
87 C38 H38B C H sing 1.09 N N
88 N19 HN19 N H sing 0.97 N N
89 C29 H29 C H sing 1.08 N N
90 C13 H13 C H sing 1.08 N N
91 N41 HN41 N H sing 0.97 N N
92 C9 H9 C H sing 1.09 N N
93 C10 H10 C H sing 1.09 N N
94 C42 H42 C H sing 1.09 N N
95 C42 H42A C H sing 1.09 N N
96 C43 H43 C H sing 1.09 N N
97 C45 H45 C H sing 1.09 N N
98 C45 H45A C H sing 1.09 N N
99 C44 H44 C H sing 1.09 N N
100 C44 H44A C H sing 1.09 N N



IBI : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
IBI 3fc2 Open in New Window Bound ligand 1 1
IBI 5v67 Open in New Window Bound ligand 1 1
IBI 5vbr Open in New Window Bound ligand 2 1