Chemical Components in the PDB

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1E8 : Summary

Code

1E8

One-letter code

X

Molecule name

1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one

Synonyms

Imbruvica
PCI-32765

Systematic names

ProgramVersionName
ACDLabs 12.01 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one
OpenEye OEToolkits 1.7.6 1-[(3R)-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]prop-2-en-1-one

Formula

C25 H24 N6 O2

Formal charge

0

Molecular weight

440.497 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1c(c2c(nc1)n(nc2c3ccc(cc3)Oc4ccccc4)C5CCCN(C5)C(=O)\C=C)N
SMILES CACTVS 3.385 Nc1ncnc2n(nc(c3ccc(Oc4ccccc4)cc3)c12)[CH]5CCCN(C5)C(=O)C=C
SMILES OpenEye OEToolkits 1.7.6 C=CC(=O)N1CCCC(C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(nc(c3ccc(Oc4ccccc4)cc3)c12)[C@@H]5CCCN(C5)C(=O)C=C
Canonical SMILES OpenEye OEToolkits 1.7.6 C=CC(=O)N1CCC[C@H](C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N

IUPAC InChI

InChI=1S/C25H24N6O2/c1-2-21(32)30-14-6-7-18(15-30)31-25-22(24(26)27-16-28-25)23(29-31)17-10-12-20(13-11-17)33-19-8-4-3-5-9-19/h2-5,8-13,16,18H,1,6-7,14-15H2,(H2,26,27,28)/t18-/m1/s1

IUPAC InChI key

XYFPWWZEPKGCCK-GOSISDBHSA-N
1E8

wwPDB Information

Atom count

57 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-12-18

Last modified at

2020-05-26

Status

Released

Obsoleted

Not Assigned



1E8 : 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 C2 C C2 N Y N 0 2.098 4.217 -0.544
2 C4 C C4 N Y N 0 1.823 1.936 -0.428
3 C5 C C5 N Y N 0 0.468 2.136 -0.104
4 C6 C C6 N Y N 0 -0.014 3.452 -0.016
5 CAA C CAA N N N 0 8.341 -2.305 1.251
6 CAD C CAD N N N 0 7.286 -2.278 0.442
7 CAE C CAE N Y N 0 -7.739 -2.398 -1.351
8 CAF C CAF N Y N 0 -8.32 -1.908 -0.196
9 CAG C CAG N Y N 0 -6.392 -2.195 -1.59
10 CAI C CAI N Y N 0 -7.556 -1.216 0.723
11 CAJ C CAJ N Y N 0 -5.625 -1.498 -0.676
12 CAK C CAK N Y N 0 -3.875 0.855 0.059
13 CAL C CAL N Y N 0 -3.128 -0.694 1.743
14 CAM C CAM N Y N 0 -2.566 1.138 -0.267
15 CAN C CAN N Y N 0 -1.816 -0.412 1.425
16 CAO C CAO N N N 0 4.487 -1.628 -2.301
17 CAP C CAP N N N 0 3.146 -0.969 -1.971
18 CAQ C CAQ N N N 0 4.93 -2.494 -1.118
19 CAR C CAR N N N 0 3.737 -0.914 0.455
20 CAW C CAW N N N 0 6.054 -1.593 0.862
21 CAY C CAY N Y N 0 -6.205 -1.011 0.486
22 CAZ C CAZ N Y N 0 -4.16 -0.058 1.066
23 CBA C CBA N Y N 0 -1.526 0.505 0.415
24 CBB C CBB N Y N 0 -0.118 0.806 0.066
25 CBE C CBE R N N 0 3.307 -0.066 -0.746
26 H2 H H2 N N N 0 2.752 5.058 -0.72
27 HAA H HAA N N N 0 8.293 -1.823 2.217
28 HAAA H HAAA N N N 0 9.245 -2.807 0.943
29 HAD H HAD N N N 0 7.334 -2.759 -0.524
30 HAE H HAE N N N 0 -8.337 -2.943 -2.066
31 HAF H HAF N N N 0 -9.373 -2.068 -0.012
32 HAG H HAG N N N 0 -5.939 -2.582 -2.491
33 HAI H HAI N N N 0 -8.011 -0.833 1.625
34 HAJ H HAJ N N N 0 -4.573 -1.34 -0.863
35 HAK H HAK N N N 0 -4.68 1.349 -0.465
36 HAL H HAL N N N 0 -3.352 -1.403 2.525
37 HAM H HAM N N N 0 -2.345 1.848 -1.05
38 HAN H HAN N N N 0 -1.013 -0.9 1.958
39 HAO H HAO N N N 0 4.377 -2.252 -3.188
40 HAOA H HAOA N N N 0 5.234 -0.857 -2.489
41 HAP H HAP N N N 0 2.816 -0.371 -2.821
42 HAPA H HAPA N N N 0 2.405 -1.739 -1.76
43 HAQ H HAQ N N N 0 4.23 -3.319 -0.986
44 HAQA H HAQA N N N 0 5.929 -2.888 -1.308
45 HAR H HAR N N N 0 3.949 -0.264 1.304
46 HARA H HARA N N N 0 2.939 -1.609 0.716
47 HBE H HBE N N N 0 4.066 0.69 -0.948
48 HNAA H HNAA N N N 0 -1.949 2.964 0.439
49 HNAB H HNAB N N N 0 -1.65 4.616 0.38
50 N1 N N1 N Y N 0 0.833 4.451 -0.243
51 N3 N N3 N Y N 0 2.593 3.003 -0.638
52 NAB N NAB N N N 0 -1.336 3.702 0.299
53 NAU N NAU N Y N 0 0.835 -0.071 -0.146
54 NBF N NBF N Y N 0 2.03 0.589 -0.45
55 NBG N NBG N N N 0 4.948 -1.664 0.095
56 OAC O OAC N N N 0 6.032 -0.963 1.902
57 OAV O OAV N N N 0 -5.451 -0.33 1.389



1E8 : 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 C2 N1 C N doub 1.32 N Y
2 N1 C6 N C sing 1.33 N Y
3 N3 C2 N C sing 1.31 N Y
4 C2 H2 C H sing 1.08 N N
5 N3 C4 N C doub 1.33 N Y
6 NBF C4 N C sing 1.36 N Y
7 C4 C5 C C sing 1.41 N Y
8 C5 C6 C C doub 1.4 N Y
9 C5 CBB C C sing 1.46 N Y
10 C6 NAB C N sing 1.38 N N
11 CAA CAD C C doub 1.33 N N
12 CAA HAA C H sing 1.08 N N
13 CAA HAAA C H sing 1.08 N N
14 NAB HNAB N H sing 0.97 N N
15 NAB HNAA N H sing 0.97 N N
16 OAC CAW O C doub 1.22 N N
17 CAD CAW C C sing 1.47 N N
18 CAD HAD C H sing 1.08 N N
19 CAF CAE C C doub 1.38 N Y
20 CAE CAG C C sing 1.38 N Y
21 CAE HAE C H sing 1.08 N N
22 CAF CAI C C sing 1.38 N Y
23 CAF HAF C H sing 1.08 N N
24 CAG CAJ C C doub 1.38 N Y
25 CAG HAG C H sing 1.08 N N
26 CAI CAY C C doub 1.39 N Y
27 CAI HAI C H sing 1.08 N N
28 CAY CAJ C C sing 1.39 N Y
29 CAJ HAJ C H sing 1.08 N N
30 CAM CAK C C doub 1.38 N Y
31 CAK CAZ C C sing 1.39 N Y
32 CAK HAK C H sing 1.08 N N
33 CAZ CAL C C doub 1.39 N Y
34 CAN CAL C C sing 1.38 N Y
35 CAL HAL C H sing 1.08 N N
36 CAM CBA C C sing 1.4 N Y
37 CAM HAM C H sing 1.08 N N
38 CBA CAN C C doub 1.39 N Y
39 CAN HAN C H sing 1.08 N N
40 CAQ CAO C C sing 1.53 N N
41 CAO CAP C C sing 1.53 N N
42 CAO HAO C H sing 1.09 N N
43 CAO HAOA C H sing 1.09 N N
44 CBE CAP C C sing 1.53 N N
45 CAP HAP C H sing 1.09 N N
46 CAP HAPA C H sing 1.09 N N
47 NBG CAQ N C sing 1.47 N N
48 CAQ HAQ C H sing 1.09 N N
49 CAQ HAQA C H sing 1.09 N N
50 NBG CAR N C sing 1.47 N N
51 CAR CBE C C sing 1.53 N N
52 CAR HAR C H sing 1.09 N N
53 CAR HARA C H sing 1.09 N N
54 NBF NAU N N sing 1.4 N Y
55 NAU CBB N C doub 1.31 N Y
56 CAZ OAV C O sing 1.36 N N
57 CAY OAV C O sing 1.36 N N
58 CAW NBG C N sing 1.35 N N
59 CBB CBA C C sing 1.48 N N
60 CBE NBF C N sing 1.47 N N
61 CBE HBE C H sing 1.09 N N



1E8 : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
1E8 4ifg Open in New Window Bound ligand 1 1
1E8 4rz7 Open in New Window Bound ligand 1 1
1E8 5p9i Open in New Window Bound ligand 1 1
1E8 5yu9 Open in New Window Bound ligand 4 1
1E8 6l8l Open in New Window Bound ligand 4 1
1E8 6yg2 Open in New Window Bound ligand 1 1
1E8 6yz4 Open in New Window Bound ligand 1 1