Chemical Components in the PDB

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IMJ : Summary

Code

IMJ

One-letter code

X

Molecule name

(2E)-N-[(1,2-dimethyl-1H-indol-3-yl)methyl]-N-methyl-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)prop-2-enamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2E)-N-[(1,2-dimethyl-1H-indol-3-yl)methyl]-N-methyl-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)prop-2-enamide
OpenEye OEToolkits 1.7.0 (E)-N-[(1,2-dimethylindol-3-yl)methyl]-N-methyl-3-(7-oxo-6,8-dihydro-5H-1,8-naphthyridin-3-yl)prop-2-enamide

Formula

C23 H24 N4 O2

Formal charge

0

Molecular weight

388.462 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2Nc1ncc(cc1CC2)\C=C\C(=O)N(C)Cc4c3ccccc3n(c4C)C
SMILES CACTVS 3.370 CN(Cc1c(C)n(C)c2ccccc12)C(=O)C=Cc3cnc4NC(=O)CCc4c3
SMILES OpenEye OEToolkits 1.7.0 Cc1c(c2ccccc2n1C)CN(C)C(=O)C=Cc3cc4c(nc3)NC(=O)CC4
Canonical SMILES CACTVS 3.370 CN(Cc1c(C)n(C)c2ccccc12)C(=O)\C=C\c3cnc4NC(=O)CCc4c3
Canonical SMILES OpenEye OEToolkits 1.7.0 Cc1c(c2ccccc2n1C)CN(C)C(=O)/C=C/c3cc4c(nc3)NC(=O)CC4

IUPAC InChI

InChI=1S/C23H24N4O2/c1-15-19(18-6-4-5-7-20(18)27(15)3)14-26(2)22(29)11-8-16-12-17-9-10-21(28)25-23(17)24-13-16/h4-8,11-13H,9-10,14H2,1-3H3,(H,24,25,28)/b11-8+

IUPAC InChI key

PVNPCRMKZHRPEV-DHZHZOJOSA-N
IMJ

wwPDB Information

Atom count

53 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-08-30

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



IMJ : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C20 C C20 N Y N 0 5.067 1.958 -0.532
2 C21 C C21 N Y N 0 5.886 2.759 0.213
3 C22 C C22 N Y N 0 6.465 2.282 1.382
4 C23 C C23 N Y N 0 6.224 0.996 1.811
5 C24 C C24 N Y N 0 5.392 0.163 1.068
6 C25 C C25 N Y N 0 4.809 0.651 -0.116
7 N26 N N26 N Y N 0 4.966 -1.136 1.226
8 C27 C C27 N Y N 0 4.141 -1.484 0.191
9 C28 C C28 N Y N 0 4.004 -0.449 -0.653
10 C29 C C29 N N N 0 5.341 -2.016 2.335
11 C30 C C30 N N N 0 3.482 -2.829 0.025
12 C31 C C31 N N N 0 3.181 -0.424 -1.914
13 N32 N N32 N N N 0 1.86 0.14 -1.624
14 C33 C C33 N N N 0 1.667 1.592 -1.628
15 C34 C C34 N N N 0 0.823 -0.677 -1.354
16 O35 O O35 N N N 0 0.983 -1.883 -1.351
17 C36 C C36 N N N 0 -0.496 -0.114 -1.064
18 C37 C C37 N N N 0 -1.534 -0.932 -0.793
19 C38 C C38 N Y N 0 -2.859 -0.366 -0.502
20 C39 C C39 N Y N 0 -3.949 -1.206 -0.219
21 C40 C C40 N Y N 0 -5.162 -0.632 0.047
22 C41 C C41 N N N 0 -6.357 -1.495 0.356
23 C42 C C42 N N N 0 -7.253 -0.78 1.368
24 C43 C C43 N N N 0 -7.487 0.64 0.927
25 N44 N N44 N N N 0 -6.523 1.336 0.299
26 C45 C C45 N Y N 0 -5.289 0.755 0.03
27 N46 N N46 N Y N 0 -4.243 1.526 -0.241
28 C47 C C47 N Y N 0 -3.056 1.019 -0.496
29 O48 O O48 N N N 0 -8.56 1.163 1.141
30 H20 H H20 N N N 0 4.617 2.337 -1.438
31 H21 H H21 N N N 0 6.086 3.77 -0.11
32 H22 H H22 N N N 0 7.11 2.927 1.959
33 H23 H H23 N N N 0 6.679 0.634 2.721
34 H29 H H29 N N N 0 4.623 -1.904 3.147
35 H29A H H29A N N N 0 5.344 -3.051 1.993
36 H29B H H29B N N N 0 6.337 -1.748 2.691
37 H30 H H30 N N N 0 2.554 -2.852 0.597
38 H30A H H30A N N N 0 3.263 -2.998 -1.029
39 H30B H H30B N N N 0 4.151 -3.609 0.387
40 H31 H H31 N N N 0 3.681 0.19 -2.663
41 H31A H H31A N N N 0 3.066 -1.439 -2.294
42 H33 H H33 N N N 0 1.296 1.907 -2.603
43 H33A H H33A N N N 0 0.945 1.865 -0.858
44 H33B H H33B N N N 0 2.618 2.086 -1.424
45 H36 H H36 N N N 0 -0.638 0.957 -1.066
46 H37 H H37 N N N 0 -1.392 -2.002 -0.791
47 H39 H H39 N N N 0 -3.832 -2.28 -0.211
48 H41 H H41 N N N 0 -6.918 -1.681 -0.56
49 H41A H H41A N N N 0 -6.021 -2.444 0.775
50 H42 H H42 N N N 0 -8.209 -1.3 1.436
51 H42A H H42A N N N 0 -6.77 -0.781 2.345
52 HN44 H HN44 N N N 0 -6.691 2.253 0.032
53 H47 H H47 N N N 0 -2.227 1.678 -0.708



IMJ : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 C21 C C doub 1.37 N Y
2 C20 C25 C C sing 1.4 N Y
3 C21 C22 C C sing 1.39 N Y
4 C22 C23 C C doub 1.38 N Y
5 C23 C24 C C sing 1.39 N Y
6 C24 C25 C C doub 1.41 N Y
7 C24 N26 C N sing 1.38 N Y
8 C25 C28 C C sing 1.47 N Y
9 N26 C27 N C sing 1.37 N Y
10 N26 C29 N C sing 1.46 N N
11 C27 C28 C C doub 1.34 N Y
12 C27 C30 C C sing 1.51 N N
13 C28 C31 C C sing 1.51 N N
14 C31 N32 C N sing 1.47 N N
15 N32 C33 N C sing 1.46 N N
16 N32 C34 N C sing 1.35 N N
17 C34 O35 C O doub 1.22 N N
18 C34 C36 C C sing 1.46 N N
19 C36 C37 C C doub 1.35 N N
20 C37 C38 C C sing 1.47 N N
21 C38 C39 C C doub 1.4 N Y
22 C38 C47 C C sing 1.4 N Y
23 C39 C40 C C sing 1.37 N Y
24 C40 C41 C C sing 1.51 N N
25 C40 C45 C C doub 1.39 N Y
26 C41 C42 C C sing 1.53 N N
27 C42 C43 C C sing 1.51 N N
28 C43 N44 C N sing 1.34 N N
29 C43 O48 C O doub 1.21 N N
30 N44 C45 N C sing 1.39 N N
31 C45 N46 C N sing 1.33 N Y
32 N46 C47 N C doub 1.32 N Y
33 C20 H20 C H sing 1.08 N N
34 C21 H21 C H sing 1.08 E N
35 C22 H22 C H sing 1.08 N N
36 C23 H23 C H sing 1.08 N N
37 C29 H29 C H sing 1.09 N N
38 C29 H29A C H sing 1.09 N N
39 C29 H29B C H sing 1.09 N N
40 C30 H30 C H sing 1.09 N N
41 C30 H30A C H sing 1.09 N N
42 C30 H30B C H sing 1.09 N N
43 C31 H31 C H sing 1.09 N N
44 C31 H31A C H sing 1.09 N N
45 C33 H33 C H sing 1.09 N N
46 C33 H33A C H sing 1.09 N N
47 C33 H33B C H sing 1.09 N N
48 C36 H36 C H sing 1.08 N N
49 C37 H37 C H sing 1.08 N N
50 C39 H39 C H sing 1.08 N N
51 C41 H41 C H sing 1.09 N N
52 C41 H41A C H sing 1.09 N N
53 C42 H42 C H sing 1.09 N N
54 C42 H42A C H sing 1.09 N N
55 N44 HN44 N H sing 0.97 N N
56 C47 H47 C H sing 1.08 N N



IMJ : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
IMJ 3oig Open in New Window Bound ligand 1 1
IMJ 3ojf Open in New Window Bound ligand 4 1