Chemical Components in the PDB

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JDH : Summary

Code

JDH

One-letter code

X

Molecule name

5-azanyl-3-[1-[[4-[(4-methylpiperazin-1-yl)methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 5-azanyl-3-[1-[[4-[(4-methylpiperazin-1-yl)methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile

Formula

C25 H27 N7

Formal charge

0

Molecular weight

425.529 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1CCN(CC1)Cc2ccc(Cn3ccc4ccc(cc34)c5n[nH]c(N)c5C#N)cc2
SMILES OpenEye OEToolkits 2.0.7 CN1CCN(CC1)Cc2ccc(cc2)Cn3ccc4c3cc(cc4)c5c(c([nH]n5)N)C#N
Canonical SMILES CACTVS 3.385 CN1CCN(CC1)Cc2ccc(Cn3ccc4ccc(cc34)c5n[nH]c(N)c5C#N)cc2
Canonical SMILES OpenEye OEToolkits 2.0.7 CN1CCN(CC1)Cc2ccc(cc2)Cn3ccc4c3cc(cc4)c5c(c([nH]n5)N)C#N

IUPAC InChI

InChI=1S/C25H27N7/c1-30-10-12-31(13-11-30)16-18-2-4-19(5-3-18)17-32-9-8-20-6-7-21(14-23(20)32)24-22(15-26)25(27)29-28-24/h2-9,14H,10-13,16-17H2,1H3,(H3,27,28,29)

IUPAC InChI key

DTFOFBCTICVEIL-UHFFFAOYSA-N
JDH

wwPDB Information

Atom count

59 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-02-19

Last modified at

2020-03-13

Status

Released

Obsoleted

Not Assigned



JDH : Atoms of Molecule

Total Number of Atoms: 59
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 4.091 2.224 1.172
2 C13 C C2 N Y N 0 1.374 4.107 -0.349
3 C15 C C3 N N N 0 0.121 2.41 -1.717
4 C17 C C4 N Y N 0 -2.036 2.701 -0.48
5 C20 C C5 N N N 0 -4.272 0.303 1.391
6 C22 C C6 N N N 0 -6.57 -0.446 1.243
7 C26 C C7 N N N 0 -6.045 -1.635 -1.309
8 C28 C C8 N Y N 0 -2.119 0.01 0.148
9 N01 N N1 N N N 0 5.934 -4.299 -0.221
10 C02 C C9 N Y N 0 4.954 -3.329 -0.134
11 N03 N N2 N Y N 0 3.623 -3.535 -0.184
12 N04 N N3 N Y N 0 2.953 -2.314 -0.063
13 C05 C C10 N Y N 0 3.831 -1.346 0.062
14 C06 C C11 N Y N 0 3.534 0.097 0.216
15 C07 C C12 N Y N 0 2.442 0.651 -0.442
16 C08 C C13 N Y N 0 2.172 2.007 -0.304
17 C09 C C14 N Y N 0 3.0 2.799 0.514
18 C11 C C15 N Y N 0 4.354 0.895 1.022
19 C12 C C16 N Y N 0 2.448 4.154 0.457
20 N14 N N4 N Y N 0 1.194 2.833 -0.813
21 C16 C C17 N Y N 0 -1.027 1.86 -0.91
22 C18 C C18 N Y N 0 -3.086 2.197 0.264
23 C19 C C19 N Y N 0 -3.127 0.852 0.579
24 N21 N N5 N N N 0 -5.35 -0.127 0.489
25 C23 C C20 N N N 0 -7.689 -0.811 0.265
26 N24 N N6 N N N 0 -7.266 -1.954 -0.555
27 C25 C C21 N N N 0 -7.076 -3.154 0.272
28 C27 C C22 N N N 0 -4.926 -1.27 -0.331
29 C29 C C23 N Y N 0 -1.072 0.513 -0.601
30 C30 C C24 N Y N 0 5.162 -1.963 0.027
31 C31 C C25 N N N 0 6.423 -1.292 0.13
32 N32 N N7 N N N 0 7.424 -0.76 0.211
33 H1 H H1 N N N 0 4.728 2.834 1.796
34 H2 H H2 N N N 0 0.747 4.951 -0.595
35 H3 H H3 N N N 0 -0.221 3.265 -2.299
36 H4 H H4 N N N 0 0.495 1.638 -2.389
37 H5 H H5 N N N 0 -2.001 3.753 -0.721
38 H6 H H6 N N N 0 -3.926 -0.55 1.976
39 H7 H H7 N N N 0 -4.646 1.076 2.062
40 H8 H H8 N N N 0 -6.378 -1.289 1.907
41 H9 H H9 N N N 0 -6.871 0.42 1.832
42 H10 H H10 N N N 0 -5.745 -2.502 -1.898
43 H11 H H11 N N N 0 -6.238 -0.793 -1.973
44 H12 H H12 N N N 0 -2.154 -1.042 0.39
45 H13 H H13 N N N 0 5.686 -5.231 -0.329
46 H14 H H14 N N N 0 6.87 -4.049 -0.174
47 H15 H H15 N N N 0 3.194 -4.399 -0.288
48 H16 H H16 N N N 0 1.812 0.033 -1.064
49 H17 H H17 N N N 0 5.2 0.455 1.529
50 H18 H H18 N N N 0 2.831 5.025 0.966
51 H24 H H24 N N N 0 -6.264 -2.983 0.978
52 H19 H H19 N N N 0 -3.874 2.855 0.601
53 H21 H H21 N N N 0 -8.588 -1.076 0.822
54 H22 H H22 N N N 0 -7.9 0.042 -0.381
55 H25 H H25 N N N 0 -7.994 -3.367 0.818
56 H26 H H26 N N N 0 -6.829 -4.001 -0.368
57 H27 H H27 N N N 0 -4.715 -2.123 0.315
58 H28 H H28 N N N 0 -4.028 -1.005 -0.888
59 H29 H H29 N N N 0 -0.284 -0.145 -0.938



JDH : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C27 C26 C C sing 1.53 N N
2 C27 N21 C N sing 1.47 N N
3 C25 N24 C N sing 1.47 N N
4 C26 N24 C N sing 1.47 N N
5 N24 C23 N C sing 1.47 N N
6 C20 N21 C N sing 1.47 N N
7 C20 C19 C C sing 1.51 N N
8 N21 C22 N C sing 1.47 N N
9 C22 C23 C C sing 1.53 N N
10 C18 C19 C C doub 1.38 N Y
11 C18 C17 C C sing 1.38 N Y
12 C19 C28 C C sing 1.38 N Y
13 C17 C16 C C doub 1.38 N Y
14 C28 C29 C C doub 1.38 N Y
15 C16 C29 C C sing 1.38 N Y
16 C16 C15 C C sing 1.51 N N
17 C13 C12 C C doub 1.34 N Y
18 C13 N14 C N sing 1.37 N Y
19 C12 C09 C C sing 1.46 N Y
20 N14 C15 N C sing 1.47 N N
21 N14 C08 N C sing 1.38 N Y
22 C09 C08 C C doub 1.41 N Y
23 C09 C10 C C sing 1.4 N Y
24 C08 C07 C C sing 1.39 N Y
25 C10 C11 C C doub 1.36 N Y
26 C07 C06 C C doub 1.39 N Y
27 C11 C06 C C sing 1.4 N Y
28 C06 C05 C C sing 1.48 N N
29 N04 C05 N C doub 1.31 N Y
30 N04 N03 N N sing 1.4 N Y
31 C05 C30 C C sing 1.47 N Y
32 C30 C31 C C sing 1.43 N N
33 C30 C02 C C doub 1.39 N Y
34 N03 C02 N C sing 1.35 N Y
35 C31 N32 C N trip 1.14 N N
36 C02 N01 C N sing 1.38 N N
37 C10 H1 C H sing 1.08 N N
38 C13 H2 C H sing 1.08 N N
39 C15 H3 C H sing 1.09 N N
40 C15 H4 C H sing 1.09 N N
41 C17 H5 C H sing 1.08 N N
42 C20 H6 C H sing 1.09 N N
43 C20 H7 C H sing 1.09 N N
44 C22 H8 C H sing 1.09 N N
45 C22 H9 C H sing 1.09 N N
46 C26 H10 C H sing 1.09 N N
47 C26 H11 C H sing 1.09 N N
48 C28 H12 C H sing 1.08 N N
49 N01 H13 N H sing 0.97 N N
50 N01 H14 N H sing 0.97 N N
51 N03 H15 N H sing 0.97 N N
52 C07 H16 C H sing 1.08 N N
53 C11 H17 C H sing 1.08 N N
54 C12 H18 C H sing 1.08 N N
55 C18 H19 C H sing 1.08 N N
56 C23 H21 C H sing 1.09 N N
57 C23 H22 C H sing 1.09 N N
58 C25 H24 C H sing 1.09 N N
59 C25 H25 C H sing 1.09 N N
60 C25 H26 C H sing 1.09 N N
61 C27 H27 C H sing 1.09 N N
62 C27 H28 C H sing 1.09 N N
63 C29 H29 C H sing 1.08 N N



JDH : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JDH 6qr8 Open in New Window Bound ligand 2 1