Chemical Components in the PDB

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D8M : Summary

Code

D8M

One-letter code

X

Molecule name

2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide (non-preferred name)
OpenEye OEToolkits 2.0.6 2-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-~{N}-(pyridin-2-ylmethyl)ethanamide

Formula

C13 H19 N3 O4

Formal charge

0

Molecular weight

281.308 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC2C(CC(=O)NCc1ccccn1)OC(C2O)CN
SMILES CACTVS 3.385 NC[CH]1O[CH](CC(=O)NCc2ccccn2)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.6 c1ccnc(c1)CNC(=O)CC2C(C(C(O2)CN)O)O
Canonical SMILES CACTVS 3.385 NC[C@H]1O[C@@H](CC(=O)NCc2ccccn2)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccnc(c1)CNC(=O)C[C@H]2[C@@H]([C@@H]([C@H](O2)CN)O)O

IUPAC InChI

InChI=1S/C13H19N3O4/c14-6-10-13(19)12(18)9(20-10)5-11(17)16-7-8-3-1-2-4-15-8/h1-4,9-10,12-13,18-19H,5-7,14H2,(H,16,17)/t9-,10+,12-,13+/m0/s1

IUPAC InChI key

BIGFPMOCLWRIMB-JULQROHOSA-N
D8M

wwPDB Information

Atom count

39 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-10-23

Last modified at

2020-04-17

Status

Released

Obsoleted

Not Assigned



D8M : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3 O O1 N N N 0 3.348 -2.683 0.079
2 C4 C C1 N Y N 0 -4.915 -0.72 0.831
3 C5 C C2 N N N 0 -2.744 0.516 0.868
4 C6 C C3 N N N 0 -0.447 -0.154 0.409
5 N1 N N1 N N N 0 -1.753 -0.221 0.081
6 C7 C C4 N N N 0 0.573 -0.912 -0.4
7 C8 C C5 S N N 0 1.968 -0.668 0.179
8 N2 N N2 N N N 0 4.011 3.161 0.264
9 C9 C C6 R N N 0 3.026 -1.472 -0.608
10 C10 C C7 S N N 0 4.252 -0.534 -0.656
11 C11 C C8 R N N 0 3.79 0.727 0.109
12 C12 C C9 N N N 0 4.363 1.986 -0.545
13 O O O2 N N N 0 -0.094 0.515 1.357
14 C3 C C10 N Y N 0 -4.118 0.275 0.297
15 N N N3 N Y N 0 -4.546 1.016 -0.706
16 C2 C C11 N Y N 0 -5.74 0.841 -1.237
17 C1 C C12 N Y N 0 -6.592 -0.134 -0.756
18 C C C13 N Y N 0 -6.177 -0.934 0.298
19 O1 O O3 N N N 0 2.35 0.714 0.004
20 O2 O O4 N N N 0 5.37 -1.136 0.001
21 H1 H H1 N N N 0 4.008 -3.227 -0.371
22 H2 H H2 N N N 0 -4.557 -1.327 1.65
23 H3 H H3 N N N 0 -2.715 0.172 1.902
24 H4 H H4 N N N 0 -2.518 1.581 0.833
25 H5 H H5 N N N 0 -2.035 -0.756 -0.677
26 H6 H H6 N N N 0 0.347 -1.978 -0.365
27 H7 H H7 N N N 0 0.544 -0.569 -1.434
28 H8 H H8 N N N 0 1.992 -0.938 1.235
29 H9 H H9 N N N 0 4.331 3.053 1.215
30 H10 H H10 N N N 0 4.379 4.006 -0.147
31 H12 H H12 N N N 0 2.669 -1.689 -1.615
32 H13 H H13 N N N 0 4.503 -0.285 -1.687
33 H14 H H14 N N N 0 4.096 0.67 1.153
34 H15 H H15 N N N 0 3.947 2.096 -1.546
35 H16 H H16 N N N 0 5.448 1.901 -0.61
36 H17 H H17 N N N 0 -6.056 1.468 -2.058
37 H18 H H18 N N N 0 -7.569 -0.273 -1.196
38 H19 H H19 N N N 0 -6.82 -1.707 0.692
39 H20 H H20 N N N 0 5.663 -1.964 -0.402



D8M : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C5 N C sing 1.46 N N
2 N1 C6 N C sing 1.35 N N
3 C5 C3 C C sing 1.51 N N
4 C7 C6 C C sing 1.51 N N
5 C7 C8 C C sing 1.53 N N
6 C6 O C O doub 1.21 N N
7 C9 O3 C O sing 1.43 N N
8 C9 C8 C C sing 1.54 N N
9 C9 C10 C C sing 1.54 N N
10 C8 O1 C O sing 1.44 N N
11 C3 N C N doub 1.32 N Y
12 C3 C4 C C sing 1.38 N Y
13 C12 N2 C N sing 1.47 N N
14 C12 C11 C C sing 1.53 N N
15 N C2 N C sing 1.32 N Y
16 O1 C11 O C sing 1.44 N N
17 C10 C11 C C sing 1.55 N N
18 C10 O2 C O sing 1.43 N N
19 C4 C C C doub 1.39 N Y
20 C2 C1 C C doub 1.38 N Y
21 C C1 C C sing 1.39 N Y
22 O3 H1 O H sing 0.97 N N
23 C4 H2 C H sing 1.08 N N
24 C5 H3 C H sing 1.09 N N
25 C5 H4 C H sing 1.09 N N
26 N1 H5 N H sing 0.97 N N
27 C7 H6 C H sing 1.09 N N
28 C7 H7 C H sing 1.09 N N
29 C8 H8 C H sing 1.09 N N
30 N2 H9 N H sing 1.01 N N
31 N2 H10 N H sing 1.01 N N
32 C9 H12 C H sing 1.09 N N
33 C10 H13 C H sing 1.09 N N
34 C11 H14 C H sing 1.09 N N
35 C12 H15 C H sing 1.09 N N
36 C12 H16 C H sing 1.09 N N
37 C2 H17 C H sing 1.08 N N
38 C1 H18 C H sing 1.08 N N
39 C H19 C H sing 1.08 N N
40 O2 H20 O H sing 0.97 N N



D8M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
D8M 5qbh Open in New Window Bound ligand 1 1