Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

B8I : Summary

Code

B8I

One-letter code

X

Molecule name

methyl 4-[4-[[6-(cyanomethyl)-2-[(1-methylpyrazol-4-yl)amino]-5-oxidanylidene-pyrido[4,3-d]pyrimidin-4-yl]amino]cyclohexyl]piperazine-1-carboxylate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 methyl 4-[4-[[6-(cyanomethyl)-2-[(1-methylpyrazol-4-yl)amino]-5-oxidanylidene-pyrido[4,3-d]pyrimidin-4-yl]amino]cyclohexyl]piperazine-1-carboxylate

Formula

C25 H32 N10 O3

Formal charge

0

Molecular weight

520.587 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COC(=O)N1CCN(CC1)[CH]2CC[CH](CC2)Nc3nc(Nc4cnn(C)c4)nc5C=CN(CC#N)C(=O)c35
SMILES OpenEye OEToolkits 2.0.7 Cn1cc(cn1)Nc2nc3c(c(n2)NC4CCC(CC4)N5CCN(CC5)C(=O)OC)C(=O)N(C=C3)CC#N
Canonical SMILES CACTVS 3.385 COC(=O)N1CCN(CC1)[C@@H]2CC[C@H](CC2)Nc3nc(Nc4cnn(C)c4)nc5C=CN(CC#N)C(=O)c35
Canonical SMILES OpenEye OEToolkits 2.0.7 Cn1cc(cn1)Nc2nc3c(c(n2)NC4CCC(CC4)N5CCN(CC5)C(=O)OC)C(=O)N(C=C3)CC#N

IUPAC InChI

InChI=1S/C25H32N10O3/c1-32-16-18(15-27-32)29-24-30-20-7-9-34(10-8-26)23(36)21(20)22(31-24)28-17-3-5-19(6-4-17)33-11-13-35(14-12-33)25(37)38-2/h7,9,15-17,19H,3-6,10-14H2,1-2H3,(H2,28,29,30,31)/t17-,19-

IUPAC InChI key

HGLZLKIEOLRRSD-UAPYVXQJSA-N
B8I

wwPDB Information

Atom count

70 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-12-07

Last modified at

2022-08-22

Status

Released

Obsoleted

Not Assigned



B8I : Atoms of Molecule

Total Number of Atoms: 70
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 -4.569 5.393 -1.111
2 C2 C C2 N Y N 0 -5.564 -2.921 -0.093
3 C3 C C3 N Y N 0 -4.351 -4.792 -0.036
4 C7 C C4 N Y N 0 -2.004 0.702 0.379
5 C8 C C5 N Y N 0 -3.141 -1.309 0.199
6 C9 C C6 N N N 0 -5.69 1.314 0.036
7 C10 C C7 N N N 0 -5.703 2.658 0.08
8 C11 C C8 N N N 0 -3.346 2.828 0.319
9 C12 C C9 N N N 0 8.599 -0.653 -0.439
10 C13 C C10 N N N 0 2.792 0.788 1.478
11 C14 C C11 N N N 0 2.299 -0.381 -0.674
12 C15 C C12 N N N 0 1.465 1.541 1.373
13 C16 C C13 N N N 0 0.972 0.372 -0.779
14 C19 C C14 N N N 0 5.564 0.513 0.977
15 C20 C C15 N N N 0 5.127 -0.554 -1.157
16 C21 C C16 N N N 0 3.318 0.481 0.074
17 C22 C C17 N N N 0 0.447 0.679 0.625
18 C24 C C18 N N N 0 10.832 0.081 -0.024
19 N26 N N1 N N N 0 -4.49 5.807 -2.166
20 N29 N N2 N Y N 0 -2.01 -0.627 0.333
21 C4 C C19 N Y N 0 -3.235 1.375 0.28
22 C5 C C20 N Y N 0 -4.265 -3.438 0.018
23 C6 C C21 N Y N 0 -4.417 0.607 0.138
24 C17 C C22 N N N 0 6.809 -0.349 1.21
25 C18 C C23 N N N 0 6.355 -1.461 -1.011
26 C23 C C24 N N N 0 -6.214 -6.469 -0.274
27 C25 C C25 N N N 0 -4.67 4.857 0.256
28 N27 N N3 N Y N 0 -6.398 -3.922 -0.208
29 N28 N N4 N Y N 0 -4.325 -0.719 0.103
30 N30 N N5 N Y N 0 -5.664 -5.114 -0.175
31 N31 N N6 N N N 0 -4.565 3.396 0.217
32 N32 N N7 N N N 0 7.306 -0.815 -0.094
33 N33 N N8 N N N 0 4.592 -0.242 0.175
34 N34 N N9 N N N 0 -3.083 -2.688 0.159
35 N35 N N10 N N N 0 -0.824 1.4 0.524
36 H1 H H1 N N N 0 -5.831 -1.874 -0.08
37 O36 O O1 N N N 0 -2.351 3.52 0.44
38 O37 O O2 N N N 0 8.992 -1.043 -1.521
39 O38 O O3 N N N 0 9.455 -0.06 0.414
40 H2 H H2 N N N 0 -3.526 -5.487 0.022
41 H8 H H8 N N N 0 2.673 -0.6 -1.674
42 H3 H H3 N N N 0 -6.613 0.762 -0.073
43 H4 H H4 N N N 0 -6.65 3.172 0.004
44 H5 H H5 N N N 0 3.518 1.402 2.011
45 H6 H H6 N N N 0 2.638 -0.145 2.02
46 H7 H H7 N N N 0 2.145 -1.314 -0.132
47 H9 H H9 N N N 0 1.091 1.76 2.373
48 H10 H H10 N N N 0 1.619 2.474 0.831
49 H11 H H11 N N N 0 1.126 1.305 -1.321
50 H12 H H12 N N N 0 0.247 -0.242 -1.312
51 H13 H H13 N N N 0 5.119 0.775 1.936
52 H14 H H14 N N N 0 5.846 1.422 0.446
53 H15 H H15 N N N 0 5.415 0.37 -1.658
54 H16 H H16 N N N 0 4.365 -1.065 -1.745
55 H17 H H17 N N N 0 3.471 1.414 -0.468
56 H21 H H21 N N N 0 11.413 0.574 0.755
57 H18 H H18 N N N 0 0.293 -0.254 1.167
58 H19 H H19 N N N 0 11.252 -0.905 -0.222
59 H20 H H20 N N N 0 10.864 0.679 -0.935
60 H22 H H22 N N N 0 7.578 0.244 1.704
61 H23 H H23 N N N 0 6.55 -1.205 1.833
62 H24 H H24 N N N 0 6.051 -2.425 -0.604
63 H25 H H25 N N N 0 6.824 -1.602 -1.985
64 H26 H H26 N N N 0 -6.249 -6.771 -1.321
65 H27 H H27 N N N 0 -5.58 -7.159 0.282
66 H28 H H28 N N N 0 -7.221 -6.483 0.143
67 H29 H H29 N N N 0 -3.864 5.263 0.867
68 H30 H H30 N N N 0 -5.63 5.141 0.688
69 H32 H H32 N N N 0 -2.227 -3.139 0.227
70 H33 H H33 N N N 0 -0.836 2.369 0.559



B8I : Chemical Bonds

Total Number of Bonds: 74
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O37 C12 O C doub 1.22 N N
2 C18 C20 C C sing 1.53 N N
3 C18 N32 C N sing 1.47 N N
4 C12 N32 C N sing 1.35 N N
5 C12 O38 C O sing 1.35 N N
6 C20 N33 C N sing 1.47 N N
7 N32 C17 N C sing 1.47 N N
8 C24 O38 C O sing 1.45 N N
9 N33 C21 N C sing 1.47 N N
10 N33 C19 N C sing 1.47 N N
11 C17 C19 C C sing 1.53 N N
12 C21 C13 C C sing 1.53 N N
13 C21 C14 C C sing 1.53 N N
14 C13 C15 C C sing 1.53 N N
15 C15 C22 C C sing 1.53 N N
16 C14 C16 C C sing 1.53 N N
17 C16 C22 C C sing 1.53 N N
18 C22 N35 C N sing 1.46 N N
19 N26 C1 N C trip 1.14 N N
20 O36 C11 O C doub 1.22 N N
21 N35 C7 N C sing 1.38 N N
22 C1 C25 C C sing 1.47 N N
23 C25 N31 C N sing 1.47 N N
24 C11 N31 C N sing 1.35 N N
25 C11 C4 C C sing 1.46 N N
26 C7 C4 C C doub 1.41 N Y
27 C7 N29 C N sing 1.33 N Y
28 N31 C10 N C sing 1.36 N N
29 C4 C6 C C sing 1.42 N Y
30 N29 C8 N C doub 1.33 N Y
31 C2 N27 C N doub 1.31 N Y
32 C2 C5 C C sing 1.4 N Y
33 N27 N30 N N sing 1.4 N Y
34 C10 C9 C C doub 1.34 N N
35 C6 C9 C C sing 1.46 N N
36 C6 N28 C N doub 1.33 N Y
37 C8 N28 C N sing 1.33 N Y
38 C8 N34 C N sing 1.38 N N
39 C5 N34 C N sing 1.41 N N
40 C5 C3 C C doub 1.36 N Y
41 N30 C23 N C sing 1.47 N N
42 N30 C3 N C sing 1.36 N Y
43 C2 H1 C H sing 1.08 N N
44 C3 H2 C H sing 1.08 N N
45 C9 H3 C H sing 1.08 N N
46 C10 H4 C H sing 1.08 N N
47 C13 H5 C H sing 1.09 N N
48 C13 H6 C H sing 1.09 N N
49 C14 H7 C H sing 1.09 N N
50 C14 H8 C H sing 1.09 N N
51 C15 H9 C H sing 1.09 N N
52 C15 H10 C H sing 1.09 N N
53 C16 H11 C H sing 1.09 N N
54 C16 H12 C H sing 1.09 N N
55 C19 H13 C H sing 1.09 N N
56 C19 H14 C H sing 1.09 N N
57 C20 H15 C H sing 1.09 N N
58 C20 H16 C H sing 1.09 N N
59 C21 H17 C H sing 1.09 N N
60 C22 H18 C H sing 1.09 N N
61 C24 H19 C H sing 1.09 N N
62 C24 H20 C H sing 1.09 N N
63 C24 H21 C H sing 1.09 N N
64 C17 H22 C H sing 1.09 N N
65 C17 H23 C H sing 1.09 N N
66 C18 H24 C H sing 1.09 N N
67 C18 H25 C H sing 1.09 N N
68 C23 H26 C H sing 1.09 N N
69 C23 H27 C H sing 1.09 N N
70 C23 H28 C H sing 1.09 N N
71 C25 H29 C H sing 1.09 N N
72 C25 H30 C H sing 1.09 N N
73 N34 H32 N H sing 0.97 N N
74 N35 H33 N H sing 0.97 N N



B8I : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
B8I 7qg1 Open in New Window Bound ligand 2 1