Chemical Components in the PDB

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A5B : Summary

Code

A5B

One-letter code

X

Molecule name

alisertib

Systematic names

ProgramVersionName
ACDLabs 12.01 4-{[9-chloro-7-(2-fluoro-6-methoxyphenyl)-5H-pyrimido[5,4-d][2]benzazepin-2-yl]amino}-2-methoxybenzoic acid
OpenEye OEToolkits 2.0.4 4-[[9-chloranyl-7-(2-fluoranyl-6-methoxy-phenyl)-5~{H}-pyrimido[5,4-d][2]benzazepin-2-yl]amino]-2-methoxy-benzoic acid

Formula

C27 H20 Cl F N4 O4

Formal charge

0

Molecular weight

518.924 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 COc1cc(ccc1C(O)=O)Nc2nc3c(cn2)CN=C(c4c3ccc(Cl)c4)c5c(F)cccc5OC
SMILES CACTVS 3.385 COc1cccc(F)c1C2=NCc3cnc(Nc4ccc(C(O)=O)c(OC)c4)nc3c5ccc(Cl)cc25
SMILES OpenEye OEToolkits 2.0.4 COc1cccc(c1C2=NCc3cnc(nc3-c4c2cc(cc4)Cl)Nc5ccc(c(c5)OC)C(=O)O)F
Canonical SMILES CACTVS 3.385 COc1cccc(F)c1C2=NCc3cnc(Nc4ccc(C(O)=O)c(OC)c4)nc3c5ccc(Cl)cc25
Canonical SMILES OpenEye OEToolkits 2.0.4 COc1cccc(c1C2=NCc3cnc(nc3-c4c2cc(cc4)Cl)Nc5ccc(c(c5)OC)C(=O)O)F

IUPAC InChI

InChI=1S/C27H20ClFN4O4/c1-36-21-5-3-4-20(29)23(21)25-19-10-15(28)6-8-17(19)24-14(12-30-25)13-31-27(33-24)32-16-7-9-18(26(34)35)22(11-16)37-2/h3-11,13H,12H2,1-2H3,(H,34,35)(H,31,32,33)

IUPAC InChI key

ZLHFILGSQDJULK-UHFFFAOYSA-N
A5B

wwPDB Information

Atom count

57 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-02-21

Last modified at

2016-11-04

Status

Released

Obsoleted

Not Assigned



A5B : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C27 N N N 0 2.009 -3.165 2.249
2 C10 C C11 N Y N 0 0.374 0.198 -1.715
3 C11 C C10 N Y N 0 -0.904 -0.243 -2.022
4 C12 C C9 N Y N 0 -1.684 0.732 -0.087
5 C13 C C13 N Y N 0 0.572 0.924 -0.552
6 C14 C C14 N Y N 0 1.893 1.459 -0.158
7 C15 C C19 N Y N 0 3.088 0.762 -0.344
8 C16 C C18 N Y N 0 4.295 1.355 0.053
9 C17 C C17 N Y N 0 4.305 2.608 0.627
10 C18 C C16 N Y N 0 3.117 3.295 0.816
11 C19 C C15 N Y N 0 1.923 2.73 0.428
12 C2 C C26 N Y N 0 3.656 -2.373 0.731
13 C20 C C8 N Y N 0 -4.043 0.656 0.375
14 C21 C C7 N Y N 0 -4.411 0.711 -0.967
15 C22 C C6 N Y N 0 -5.676 0.374 -1.351
16 C23 C C4 N Y N 0 -6.616 -0.027 -0.395
17 C24 C C2 N Y N 0 -6.252 -0.079 0.96
18 C25 C C3 N Y N 0 -4.965 0.26 1.337
19 C26 C C1 N N N 0 -6.712 -0.501 3.252
20 C27 C C5 N N N 0 -7.98 -0.391 -0.808
21 C3 C C25 N Y N 0 4.537 -3.279 1.301
22 C4 C C24 N Y N 0 5.84 -3.358 0.848
23 C5 C C23 N Y N 0 6.275 -2.539 -0.181
24 C6 C C22 N Y N 0 5.408 -1.635 -0.764
25 C7 C C21 N Y N 0 4.088 -1.546 -0.314
26 C8 C C20 N N N 0 3.154 -0.582 -0.933
27 C9 C C12 N N N 0 1.513 -0.135 -2.636
28 CL1 CL CL1 N N N 0 5.809 3.325 1.115
29 F1 F F1 N N N 0 5.836 -0.839 -1.768
30 H1 H H1 N N N 0 -7.531 -0.827 3.894
31 H10 H H10 N N N 0 1.13 -0.658 -3.513
32 H11 H H11 N N N 0 2.007 0.784 -2.95
33 H12 H H12 N N N 0 1.0 3.271 0.578
34 H13 H H13 N N N 0 3.128 4.276 1.268
35 H14 H H14 N N N 0 5.225 0.824 -0.092
36 H15 H H15 N N N 0 7.295 -2.608 -0.528
37 H16 H H16 N N N 0 6.523 -4.062 1.299
38 H17 H H17 N N N 0 4.206 -3.921 2.103
39 H18 H H18 N N N 0 0.964 -2.998 2.511
40 H19 H H19 N N N 0 2.144 -4.2 1.935
41 H2 H H2 N N N 0 -5.88 -1.199 3.344
42 H20 H H20 N N N 0 2.638 -2.964 3.117
43 H3 H H3 N N N 0 -6.387 0.494 3.554
44 H4 H H4 N N N 0 -4.677 0.218 2.377
45 H5 H H5 N N N 0 -9.234 -0.587 -2.333
46 H6 H H6 N N N 0 -5.953 0.416 -2.395
47 H7 H H7 N N N 0 -3.689 1.02 -1.709
48 H8 H H8 N N N 0 -2.595 1.434 1.611
49 H9 H H9 N N N 0 -1.085 -0.809 -2.924
50 N1 N N4 N N N 0 2.47 -0.989 -1.94
51 N2 N N3 N Y N 0 -1.898 0.039 -1.196
52 N3 N N2 N Y N 0 -0.479 1.168 0.24
53 N4 N N1 N N N 0 -2.75 1.003 0.756
54 O1 O O4 N N N 0 2.378 -2.291 1.181
55 O2 O O1 N N N 0 -7.157 -0.466 1.895
56 O3 O O3 N N N 0 -8.327 -0.339 -2.11
57 O4 O O2 N N N 0 -8.795 -0.738 0.024



A5B : Chemical Bonds

Total Number of Bonds: 61
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C11 N2 C N doub 1.32 N Y
2 C11 C10 C C sing 1.39 N Y
3 N2 C12 N C sing 1.33 N Y
4 C9 C10 C C sing 1.5 N N
5 C9 N1 C N sing 1.46 N N
6 C10 C13 C C doub 1.39 N Y
7 C12 N4 C N sing 1.39 N N
8 C12 N3 C N doub 1.32 N Y
9 N4 C20 N C sing 1.39 N N
10 C13 N3 C N sing 1.34 N Y
11 C13 C14 C C sing 1.48 N N
12 N1 C8 N C doub 1.28 N N
13 C1 O1 C O sing 1.43 N N
14 C21 C20 C C doub 1.39 N Y
15 C21 C22 C C sing 1.36 N Y
16 C20 C25 C C sing 1.39 N Y
17 O1 C2 O C sing 1.36 N N
18 C14 C19 C C doub 1.4 N Y
19 C14 C15 C C sing 1.4 N Y
20 C19 C18 C C sing 1.38 N Y
21 C8 C15 C C sing 1.47 N N
22 C8 C7 C C sing 1.48 N N
23 C15 C16 C C doub 1.4 N Y
24 C22 C23 C C doub 1.4 N Y
25 C25 C24 C C doub 1.38 N Y
26 C18 C17 C C doub 1.39 N Y
27 C16 C17 C C sing 1.38 N Y
28 C2 C7 C C doub 1.4 N Y
29 C2 C3 C C sing 1.39 N Y
30 C7 C6 C C sing 1.4 N Y
31 C17 CL1 C CL sing 1.74 N N
32 C23 C24 C C sing 1.4 N Y
33 C23 C27 C C sing 1.47 N N
34 C24 O2 C O sing 1.36 N N
35 C3 C4 C C doub 1.38 N Y
36 O4 C27 O C doub 1.22 N N
37 C6 F1 C F sing 1.35 N N
38 C6 C5 C C doub 1.38 N Y
39 C27 O3 C O sing 1.35 N N
40 O2 C26 O C sing 1.43 N N
41 C4 C5 C C sing 1.39 N Y
42 C26 H1 C H sing 1.09 N N
43 C26 H2 C H sing 1.09 N N
44 C26 H3 C H sing 1.09 N N
45 C25 H4 C H sing 1.08 N N
46 O3 H5 O H sing 0.97 N N
47 C22 H6 C H sing 1.08 N N
48 C21 H7 C H sing 1.08 N N
49 N4 H8 N H sing 0.97 N N
50 C11 H9 C H sing 1.08 N N
51 C9 H10 C H sing 1.09 N N
52 C9 H11 C H sing 1.09 N N
53 C19 H12 C H sing 1.08 N N
54 C18 H13 C H sing 1.08 N N
55 C16 H14 C H sing 1.08 N N
56 C5 H15 C H sing 1.08 N N
57 C4 H16 C H sing 1.08 N N
58 C3 H17 C H sing 1.08 N N
59 C1 H18 C H sing 1.09 N N
60 C1 H19 C H sing 1.09 N N
61 C1 H20 C H sing 1.09 N N



A5B : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
A5B 5ia0 Open in New Window Bound ligand 3 1