Chemical Components in the PDB

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EJB : Summary

Code

EJB

One-letter code

X

Molecule name

7-[5-S-(4-{[(2-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 7-[5-S-(4-{[(2-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine
OpenEye OEToolkits 2.0.7 (2~{R},3~{R},4~{S},5~{S})-2-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-5-[4-[(2-ethylpyridin-3-yl)methylamino]butylsulfanylmethyl]oxolane-3,4-diol

Formula

C23 H32 N6 O3 S

Formal charge

0

Molecular weight

472.604 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CCc1ncccc1CNCCCCSCC1OC(n2ccc3c(N)ncnc32)C(O)C1O
SMILES CACTVS 3.385 CCc1ncccc1CNCCCCSC[CH]2O[CH]([CH](O)[CH]2O)n3ccc4c(N)ncnc34
SMILES OpenEye OEToolkits 2.0.7 CCc1c(cccn1)CNCCCCSCC2C(C(C(O2)n3ccc4c3ncnc4N)O)O
Canonical SMILES CACTVS 3.385 CCc1ncccc1CNCCCCSC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3ccc4c(N)ncnc34
Canonical SMILES OpenEye OEToolkits 2.0.7 CCc1c(cccn1)CNCCCCSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3ccc4c3ncnc4N)O)O

IUPAC InChI

InChI=1S/C23H32N6O3S/c1-2-17-15(6-5-9-26-17)12-25-8-3-4-11-33-13-18-19(30)20(31)23(32-18)29-10-7-16-21(24)27-14-28-22(16)29/h5-7,9-10,14,18-20,23,25,30-31H,2-4,8,11-13H2,1H3,(H2,24,27,28)/t18-,19-,20-,23-/m1/s1

IUPAC InChI key

SBQBBUZLJIAJBR-GLHSZLCASA-N
EJB

wwPDB Information

Atom count

65 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-12-08

Last modified at

2021-12-17

Status

Released

Obsoleted

Not Assigned



EJB : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C17 C C1 N Y N 0 9.019 -1.216 0.49
2 C20 C C2 N Y N 0 11.045 -0.228 0.966
3 C21 C C3 N Y N 0 10.8 0.796 0.071
4 C22 C C4 N Y N 0 9.607 0.806 -0.635
5 C11 C C5 N N N 0 1.507 1.288 0.163
6 C12 C C6 N N N 0 2.593 0.751 -0.772
7 C14 C C7 N N N 0 5.028 0.234 -0.985
8 C19 C C8 N N N 0 8.332 -3.485 -0.237
9 C1 C C9 N Y N 0 -8.689 -0.757 -1.105
10 O1 O O1 N N N 0 -3.818 4.016 0.628
11 C8 C C10 S N N 0 -3.614 2.645 0.977
12 C7 C C11 R N N 0 -4.929 1.847 0.826
13 O O O2 N N N 0 -5.984 2.701 0.379
14 C9 C C12 S N N 0 -2.648 1.97 -0.022
15 O2 O O3 N N N 0 -3.166 0.633 -0.19
16 C6 C C13 R N N 0 -4.602 0.785 -0.247
17 N3 N N1 N Y N 0 -5.262 -0.484 0.073
18 C2 C C14 N Y N 0 -6.548 -0.805 -0.262
19 N2 N N2 N Y N 0 -7.521 -0.179 -0.922
20 N1 N N3 N Y N 0 -8.964 -1.968 -0.655
21 C5 C C15 N Y N 0 -4.68 -1.523 0.753
22 C4 C C16 N Y N 0 -5.557 -2.532 0.877
23 C3 C C17 N Y N 0 -6.793 -2.102 0.225
24 C C C18 N Y N 0 -8.055 -2.675 0.011
25 N N N4 N N N 0 -8.348 -3.943 0.48
26 C10 C C19 N N N 0 -1.232 1.925 0.554
27 S S S1 N N N 0 -0.092 1.265 -0.693
28 C13 C C20 N N N 0 3.942 0.771 -0.05
29 N4 N N5 N N N 0 6.323 0.253 -0.292
30 C15 C C21 N N N 0 7.393 -0.257 -1.161
31 C16 C C22 N Y N 0 8.703 -0.223 -0.417
32 N5 N N6 N Y N 0 10.162 -1.19 1.147
33 C18 C C23 N N N 0 8.044 -2.339 0.735
34 H1 H H1 N N N 0 11.97 -0.241 1.523
35 H2 H H2 N N N 0 11.527 1.582 -0.074
36 H3 H H3 N N N 0 9.389 1.594 -1.341
37 H4 H H4 N N N 0 1.452 0.661 1.053
38 H5 H H5 N N N 0 1.749 2.31 0.452
39 H6 H H6 N N N 0 2.351 -0.271 -1.061
40 H7 H H7 N N N 0 2.648 1.377 -1.662
41 H8 H H8 N N N 0 4.786 -0.789 -1.274
42 H9 H H9 N N N 0 5.083 0.86 -1.875
43 H10 H H10 N N N 0 8.225 -3.128 -1.262
44 H11 H H11 N N N 0 9.348 -3.846 -0.082
45 H12 H H12 N N N 0 7.626 -4.297 -0.06
46 H16 H H16 N N N 0 -5.196 1.369 1.768
47 H13 H H13 N N N 0 -9.455 -0.217 -1.641
48 H14 H H14 N N N 0 -4.462 4.472 1.187
49 H15 H H15 N N N 0 -3.233 2.564 1.994
50 H17 H H17 N N N 0 -6.19 3.423 0.988
51 H18 H H18 N N N 0 -2.655 2.502 -0.974
52 H19 H H19 N N N 0 -4.907 1.134 -1.233
53 H20 H H20 N N N 0 -3.669 -1.528 1.132
54 H21 H H21 N N N 0 -5.383 -3.48 1.364
55 H22 H H22 N N N 0 -9.225 -4.327 0.325
56 H23 H H23 N N N 0 -7.676 -4.447 0.965
57 H24 H H24 N N N 0 -0.921 2.931 0.834
58 H25 H H25 N N N 0 -1.219 1.283 1.435
59 H26 H H26 N N N 0 4.185 1.793 0.239
60 H27 H H27 N N N 0 3.887 0.144 0.84
61 H28 H H28 N N N 0 6.541 1.179 0.043
62 H30 H H30 N N N 0 7.167 -1.283 -1.451
63 H31 H H31 N N N 0 7.464 0.366 -2.052
64 H32 H H32 N N N 0 8.151 -2.696 1.759
65 H33 H H33 N N N 0 7.028 -1.977 0.58



EJB : Chemical Bonds

Total Number of Bonds: 68
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C8 O C sing 1.43 N N
2 O C7 O C sing 1.43 N N
3 C21 C22 C C doub 1.39 N Y
4 C21 C20 C C sing 1.38 N Y
5 C13 C14 C C sing 1.53 N N
6 C13 C12 C C sing 1.53 N N
7 C8 C7 C C sing 1.55 N N
8 C8 C9 C C sing 1.54 N N
9 C22 C16 C C sing 1.39 N Y
10 C20 N5 C N doub 1.32 N Y
11 C14 N4 C N sing 1.47 N N
12 C7 C6 C C sing 1.54 N N
13 C12 C11 C C sing 1.53 N N
14 N4 C15 N C sing 1.47 N N
15 C11 S C S sing 1.81 N N
16 C9 O2 C O sing 1.44 N N
17 C9 C10 C C sing 1.53 N N
18 C16 C17 C C doub 1.38 N Y
19 C16 C15 C C sing 1.51 N N
20 N5 C17 N C sing 1.32 N Y
21 C6 O2 C O sing 1.45 N N
22 C6 N3 C N sing 1.47 N N
23 S C10 S C sing 1.81 N N
24 C17 C18 C C sing 1.51 N N
25 N3 C5 N C sing 1.37 N Y
26 N3 C2 N C sing 1.37 N Y
27 C5 C4 C C doub 1.34 N Y
28 N2 C2 N C doub 1.33 N Y
29 N2 C1 N C sing 1.32 N Y
30 C18 C19 C C sing 1.53 N N
31 C2 C3 C C sing 1.41 N Y
32 C1 N1 C N doub 1.32 N Y
33 C4 C3 C C sing 1.46 N Y
34 C3 C C C doub 1.4 N Y
35 N1 C N C sing 1.33 N Y
36 C N C N sing 1.38 N N
37 C20 H1 C H sing 1.08 N N
38 C21 H2 C H sing 1.08 N N
39 C22 H3 C H sing 1.08 N N
40 C11 H4 C H sing 1.09 N N
41 C11 H5 C H sing 1.09 N N
42 C12 H6 C H sing 1.09 N N
43 C12 H7 C H sing 1.09 N N
44 C14 H8 C H sing 1.09 N N
45 C14 H9 C H sing 1.09 N N
46 C19 H10 C H sing 1.09 N N
47 C19 H11 C H sing 1.09 N N
48 C19 H12 C H sing 1.09 N N
49 C1 H13 C H sing 1.08 N N
50 O1 H14 O H sing 0.97 N N
51 C8 H15 C H sing 1.09 N N
52 C7 H16 C H sing 1.09 N N
53 O H17 O H sing 0.97 N N
54 C9 H18 C H sing 1.09 N N
55 C6 H19 C H sing 1.09 N N
56 C5 H20 C H sing 1.08 N N
57 C4 H21 C H sing 1.08 N N
58 N H22 N H sing 0.97 N N
59 N H23 N H sing 0.97 N N
60 C10 H24 C H sing 1.09 N N
61 C10 H25 C H sing 1.09 N N
62 C13 H26 C H sing 1.09 N N
63 C13 H27 C H sing 1.09 N N
64 N4 H28 N H sing 1.01 N N
65 C15 H30 C H sing 1.09 N N
66 C15 H31 C H sing 1.09 N N
67 C18 H32 C H sing 1.09 N N
68 C18 H33 C H sing 1.09 N N



EJB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EJB 7t39 Open in New Window Bound ligand 1 1