Chemical Components in the PDB

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0J8 : Summary

Code

0J8

One-letter code

X

Molecule name

N-(3-nitrobenzyl)-6-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-2-(trifluoromethyl)pyrido[2,3-d]pyrimidin-4-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(3-nitrobenzyl)-6-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-2-(trifluoromethyl)pyrido[2,3-d]pyrimidin-4-amine
OpenEye OEToolkits 1.7.6 N-[(3-nitrophenyl)methyl]-6-(1-piperidin-4-ylpyrazol-4-yl)-2-(trifluoromethyl)pyrido[2,3-d]pyrimidin-4-amine

Formula

C23 H21 F3 N8 O2

Formal charge

0

Molecular weight

498.46 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 [O-][N+](=O)c1cccc(c1)CNc4nc(nc5ncc(c2cn(nc2)C3CCNCC3)cc45)C(F)(F)F
SMILES CACTVS 3.370 [O-][N+](=O)c1cccc(CNc2nc(nc3ncc(cc23)c4cnn(c4)C5CCNCC5)C(F)(F)F)c1
SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)[N+](=O)[O-])CNc2c3cc(cnc3nc(n2)C(F)(F)F)c4cnn(c4)C5CCNCC5
Canonical SMILES CACTVS 3.370 [O-][N+](=O)c1cccc(CNc2nc(nc3ncc(cc23)c4cnn(c4)C5CCNCC5)C(F)(F)F)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)[N+](=O)[O-])CNc2c3cc(cnc3nc(n2)C(F)(F)F)c4cnn(c4)C5CCNCC5

IUPAC InChI

InChI=1S/C23H21F3N8O2/c24-23(25,26)22-31-20(28-10-14-2-1-3-18(8-14)34(35)36)19-9-15(11-29-21(19)32-22)16-12-30-33(13-16)17-4-6-27-7-5-17/h1-3,8-9,11-13,17,27H,4-7,10H2,(H,28,29,31,32)

IUPAC InChI key

OIYLUARXJZNDPY-UHFFFAOYSA-N
0J8

wwPDB Information

Atom count

57 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-08-10

Last modified at

2012-09-28

Status

Released

Obsoleted

Not Assigned



0J8 : 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 2.248 -3.503 -0.069
2 C4 C C4 N Y N 0 0.041 -2.843 -0.167
3 C5 C C5 N Y N 0 0.457 -1.505 0.047
4 C6 C C6 N Y N 0 1.841 -1.245 0.199
5 CAF C CAF N Y N 0 4.199 3.624 2.26
6 CAG C CAG N Y N 0 3.982 2.273 2.062
7 CAH C CAH N Y N 0 4.409 4.457 1.177
8 CAI C CAI N Y N 0 -2.17 -2.186 -0.273
9 CAJ C CAJ N Y N 0 -2.704 1.574 0.191
10 CAK C CAK N Y N 0 4.177 2.59 -0.304
11 CAL C CAL N Y N 0 -0.501 -0.487 0.101
12 CAM C CAM N Y N 0 -4.237 -0.017 -0.157
13 CAN C CAN N N N 0 -8.422 0.654 -1.208
14 CAO C CAO N N N 0 -8.458 1.365 1.108
15 CAP C CAP N N N 0 -6.907 0.446 -1.159
16 CAQ C CAQ N N N 0 -6.943 1.178 1.226
17 CAR C CAR N N N 0 3.737 0.283 0.563
18 CAY C CAY N Y N 0 3.974 1.755 0.78
19 CAZ C CAZ N Y N 0 -1.836 -0.843 -0.059
20 CBA C CBA N Y N 0 -2.897 0.194 -0.011
21 CBB C CBB N Y N 0 4.394 3.94 -0.105
22 CBG C CBG N N N 0 -6.296 1.413 -0.142
23 CBJ C CBJ N N N 0 3.26 -4.618 -0.133
24 FAC F FAC N N N 0 4.539 -4.077 -0.299
25 FAD F FAD N N N 0 3.215 -5.357 1.054
26 FAE F FAE N N N 0 2.964 -5.455 -1.214
27 H1 H H1 N N N 0 -6.69 -0.58 -0.862
28 H10 H H10 N N N 0 -6.727 0.164 1.561
29 H11 H H11 N N N 0 -6.478 2.44 -0.46
30 H12 H H12 N N N 0 -4.718 -0.968 -0.329
31 H13 H H13 N N N 0 -1.754 2.067 0.338
32 H14 H H14 N N N 0 -0.214 0.541 0.264
33 H15 H H15 N N N 0 -3.207 -2.457 -0.401
34 H16 H H16 N N N 0 1.675 0.776 0.454
35 H17 H H17 N N N 0 4.111 -0.275 1.422
36 H18 H H18 N N N 0 4.26 -0.041 -0.337
37 H19 H H19 N N N 0 4.166 2.186 -1.305
38 H2 H H2 N N N 0 -6.482 0.637 -2.144
39 H20 H H20 N N N 0 3.819 1.622 2.908
40 H21 H H21 N N N 0 4.205 4.028 3.262
41 H22 H H22 N N N 0 4.578 5.512 1.333
42 H3 H H3 N N N 0 -8.639 1.676 -1.519
43 H4 H H4 N N N 0 -8.862 -0.043 -1.921
44 H5 H H5 N N N 0 -8.841 -0.536 0.418
45 H7 H H7 N N N 0 -8.674 2.384 0.786
46 H8 H H8 N N N 0 -8.923 1.185 2.077
47 H9 H H9 N N N 0 -6.543 1.893 1.946
48 N1 N N1 N Y N 0 2.681 -2.269 0.133
49 N3 N N3 N Y N 0 0.979 -3.801 -0.216
50 NAS N NAS N Y N 0 -1.253 -3.124 -0.32
51 NAT N NAT N Y N 0 -3.874 2.156 0.166
52 NAW N NAW N N N 0 -8.994 0.417 0.123
53 NAX N NAX N N N 0 2.301 0.037 0.409
54 NBH N NBH N N N 1 4.612 4.833 -1.265
55 NBI N NBI N Y N 0 -4.853 1.178 -0.047
56 OAA O OAA N N N 0 4.6 4.378 -2.395
57 OAB O OAB N N N -1 4.803 6.023 -1.09



0J8 : 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 CAO NAW C N sing 1.4684091 N N
2 CAO CAQ C C sing 1.5310513 N N
3 NAW CAN N C sing 1.4679625 N N
4 CAQ CBG C C sing 1.5314236 N N
5 CAN CAP C C sing 1.5299968 N N
6 CBG CAP C C sing 1.5305878 N N
7 CBG NBI C N sing 1.4650935 N N
8 NAT NBI N N sing 1.400105 N Y
9 NAT CAJ N C doub 1.307 N Y
10 NBI CAM N C sing 1.3489184 N Y
11 CAJ CBA C C sing 1.407996 N Y
12 CAM CBA C C doub 1.364345 N Y
13 CBA CAZ C C sing 1.4843833 N N
14 CAZ CAI C C doub 1.4003575 N Y
15 CAZ CAL C C sing 1.390885 N Y
16 CAI NAS C N sing 1.3126088 N Y
17 CAL C5 C C doub 1.3989296 N Y
18 NAS C4 N C doub 1.3329688 N Y
19 C5 C4 C C sing 1.4174259 N Y
20 C5 C6 C C sing 1.4163898 N Y
21 C4 N3 C N sing 1.3416442 N Y
22 NAX C6 N C sing 1.3781234 N N
23 NAX CAR N C sing 1.4650352 N N
24 C6 N1 C N doub 1.3260965 N Y
25 N3 C2 N C doub 1.3117827 N Y
26 CAR CAY C C sing 1.5066658 N N
27 N1 C2 N C sing 1.3232721 N Y
28 C2 CBJ C C sing 1.507138 N N
29 FAE CBJ F C sing 1.3988373 N N
30 CAY CAG C C doub 1.382719 N Y
31 CAY CAK C C sing 1.3832896 N Y
32 CAG CAF C C sing 1.3825679 N Y
33 CBJ FAD C F sing 1.3989693 N N
34 CBJ FAC C F sing 1.3985986 N N
35 CAK CBB C C doub 1.3817344 N Y
36 CAF CAH C C doub 1.3823451 N Y
37 CBB CAH C C sing 1.382403 N Y
38 CBB NBH C N sing 1.4800584 N N
39 NBH OAA N O doub 1.2182237 N N
40 NBH OAB N O sing 1.2178694 N N
41 CAP H1 C H sing 1.0899422 N N
42 CAP H2 C H sing 1.0896472 N N
43 CAN H3 C H sing 1.090089 N N
44 CAN H4 C H sing 1.0898523 N N
45 NAW H5 N H sing 1.0092784 N N
46 CAO H7 C H sing 1.0902756 N N
47 CAO H8 C H sing 1.0897642 N N
48 CAQ H9 C H sing 1.0906993 N N
49 CAQ H10 C H sing 1.0895306 N N
50 CBG H11 C H sing 1.0904022 N N
51 CAM H12 C H sing 1.0795119 N N
52 CAJ H13 C H sing 1.0803509 N N
53 CAL H14 C H sing 1.079686 N N
54 CAI H15 C H sing 1.0794415 N N
55 NAX H16 N H sing 0.96954733 N N
56 CAR H17 C H sing 1.0904683 N N
57 CAR H18 C H sing 1.0901858 N N
58 CAK H19 C H sing 1.0795082 N N
59 CAG H20 C H sing 1.0798546 N N
60 CAF H21 C H sing 1.0803962 N N
61 CAH H22 C H sing 1.0797787 N N



0J8 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0J8 4gg7 Open in New Window Bound ligand 1 1