Chemical Components in the PDB

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7MC : Summary

Code

7MC

One-letter code

X

Molecule name

5'-O-[(R)-[(N-acetyl-L-alpha-aspartyl)amino](3-aminopropoxy)phosphoryl]adenosine

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-O-[(R)-[(N-acetyl-L-alpha-aspartyl)amino](3-aminopropoxy)phosphoryl]adenosine
OpenEye OEToolkits 1.7.0 (3S)-3-acetamido-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-(3-azanylpropoxy)phosphoryl]amino]-4-oxo-butanoic acid

Formula

C19 H29 N8 O10 P

Formal charge

0

Molecular weight

560.455 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CC(NC(=O)C)C(=O)NP(=O)(OCCCN)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.370 CC(=O)N[CH](CC(O)=O)C(=O)N[P](=O)(OCCCN)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.7.0 CC(=O)NC(CC(=O)O)C(=O)NP(=O)(OCCCN)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Canonical SMILES CACTVS 3.370 CC(=O)N[C@@H](CC(O)=O)C(=O)N[P@@](=O)(OCCCN)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 1.7.0 CC(=O)N[C@@H](CC(=O)O)C(=O)N[P@@](=O)(OCCCN)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

IUPAC InChI

InChI=1S/C19H29N8O10P/c1-9(28)25-10(5-12(29)30)18(33)26-38(34,35-4-2-3-20)36-6-11-14(31)15(32)19(37-11)27-8-24-13-16(21)22-7-23-17(13)27/h7-8,10-11,14-15,19,31-32H,2-6,20H2,1H3,(H,25,28)(H,29,30)(H2,21,22,23)(H,26,33,34)/t10-,11+,14+,15+,19+,38+/m0/s1

IUPAC InChI key

VQAWDXQIQSFFEO-HRINIYQMSA-N
7MC

wwPDB Information

Atom count

67 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-04-18

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



7MC : Atoms of Molecule

Total Number of Atoms: 67
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 -2.376 0.771 0.236
2 N N N N N N 0 -1.922 3.076 -0.374
3 O O O N N N 0 -1.965 0.501 -0.872
4 P P P R N N 0 -2.736 -1.774 0.564
5 N1 N N1 N Y N 0 7.305 1.046 -1.267
6 C2 C C2 N Y N 0 7.167 -0.264 -1.165
7 N3 N N3 N Y N 0 6.022 -0.831 -0.849
8 C4 C C4 N Y N 0 4.942 -0.092 -0.616
9 C5 C C5 N Y N 0 5.037 1.307 -0.711
10 C6 C C6 N Y N 0 6.281 1.865 -1.052
11 N6 N N6 N N N 0 6.435 3.236 -1.162
12 N7 N N7 N Y N 0 3.812 1.811 -0.43
13 C8 C C8 N Y N 0 2.99 0.834 -0.174
14 N8 N N8 N N N 0 -2.79 -0.212 1.06
15 N9 N N9 N Y N 0 3.64 -0.36 -0.275
16 CA C CA S N N 0 -2.42 2.206 0.695
17 CB C CB N N N 0 -3.862 2.59 1.034
18 CG C CG N N N 0 -3.888 3.978 1.619
19 C1' C C1' R N N 0 3.055 -1.686 -0.061
20 O1P O O1P N N N 0 -3.24 -2.653 1.643
21 C2' C C2' R N N 0 3.3 -2.162 1.393
22 O2' O O2' N N N 0 4.568 -2.81 1.511
23 C3' C C3' S N N 0 2.142 -3.168 1.605
24 O3' O O3' N N N 0 2.598 -4.506 1.394
25 O31 O O31 N N N 0 -3.654 -1.953 -0.747
26 C32 C C32 N N N 0 -5.081 -1.879 -0.713
27 C33 C C33 N N N 0 -5.636 -2.092 -2.123
28 C34 C C34 N N N 0 -7.164 -2.013 -2.087
29 N35 N N35 N N N 0 -7.696 -2.217 -3.441
30 C36 C C36 N N N 0 -0.603 3.338 -0.47
31 C37 C C37 N N N 0 -0.104 4.321 -1.497
32 O38 O O38 N N N 0 0.181 2.782 0.27
33 C4' C C4' R N N 0 1.101 -2.776 0.538
34 O4' O O4' N N N 0 1.615 -1.628 -0.159
35 C5' C C5' N N N 0 -0.226 -2.423 1.212
36 HN H HN N N N 0 -2.541 3.463 -1.012
37 O5' O O5' N N N 0 -1.216 -2.174 0.212
38 OD1 O OD1 N N N 0 -5.061 4.572 1.888
39 OD2 O OD2 N N N 0 -2.852 4.558 1.847
40 H2 H H2 N N N 0 8.025 -0.893 -1.348
41 HN6 H HN6 N N N 0 7.299 3.609 -1.398
42 HN6A H HN6A N N N 0 5.68 3.823 -1.002
43 H8 H H8 N N N 0 1.947 0.953 0.082
44 HN8 H HN8 N N N 0 -3.119 0.004 1.947
45 HA H HA N N N 0 -1.795 2.324 1.58
46 HB H HB N N N 0 -4.467 2.566 0.128
47 HBA H HBA N N N 0 -4.265 1.883 1.759
48 H1' H H1' N N N 0 3.462 -2.403 -0.774
49 H2' H H2' N N N 0 3.225 -1.329 2.093
50 HO2' H HO2' N N N 0 4.766 -3.126 2.403
51 H3' H H3' N N N 0 1.722 -3.062 2.605
52 HO3' H HO3' N N N 0 3.296 -4.784 2.003
53 H32 H H32 N N N 0 -5.469 -2.652 -0.049
54 H32A H H32A N N N 0 -5.386 -0.899 -0.347
55 HN3A H HN3A N N N 0 -7.301 -1.552 -4.089
56 H33 H H33 N N N 0 -5.248 -1.319 -2.787
57 H33A H H33A N N N 0 -5.331 -3.072 -2.489
58 H34 H H34 N N N 0 -7.552 -2.786 -1.423
59 H34A H H34A N N N 0 -7.468 -1.033 -1.72
60 HN35 H HN35 N N N 0 -8.704 -2.17 -3.443
61 H37 H H37 N N N 0 -0.947 4.715 -2.064
62 H37A H H37A N N N 0 0.411 5.141 -0.995
63 H37B H H37B N N N 0 0.587 3.819 -2.174
64 H4' H H4' N N N 0 0.958 -3.6 -0.16
65 H5' H H5' N N N 0 -0.546 -3.254 1.841
66 H5'A H H5'A N N N 0 -0.097 -1.531 1.826
67 HOD1 H HOD1 N N N 0 -5.028 5.463 2.262



7MC : Chemical Bonds

Total Number of Bonds: 69
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CA C C C sing 1.51 N N
2 C N8 C N sing 1.35 N N
3 C O C O doub 1.21 N N
4 C36 N C N sing 1.35 N N
5 N CA N C sing 1.47 N N
6 N HN N H sing 0.97 N N
7 N8 P N P sing 1.64 N N
8 O1P P O P doub 1.48 N N
9 P O5' P O sing 1.61 N N
10 P O31 P O sing 1.61 N N
11 C2 N1 C N doub 1.32 N Y
12 N1 C6 N C sing 1.33 N Y
13 N3 C2 N C sing 1.32 N Y
14 C2 H2 C H sing 1.08 N N
15 N3 C4 N C doub 1.33 N Y
16 N9 C4 N C sing 1.37 N Y
17 C4 C5 C C sing 1.41 N Y
18 C5 N7 C N sing 1.35 N Y
19 C5 C6 C C doub 1.41 N Y
20 C6 N6 C N sing 1.38 N N
21 N6 HN6 N H sing 0.97 N N
22 N6 HN6A N H sing 0.97 N N
23 C8 N7 C N doub 1.3 N Y
24 N9 C8 N C sing 1.36 N Y
25 C8 H8 C H sing 1.08 N N
26 N8 HN8 N H sing 0.97 N N
27 C1' N9 C N sing 1.47 N N
28 CA CB C C sing 1.53 N N
29 CA HA C H sing 1.09 N N
30 CB CG C C sing 1.51 N N
31 CB HB C H sing 1.09 N N
32 CB HBA C H sing 1.09 N N
33 CG OD2 C O doub 1.21 N N
34 CG OD1 C O sing 1.34 N N
35 O4' C1' O C sing 1.44 N N
36 C1' C2' C C sing 1.55 N N
37 C1' H1' C H sing 1.09 N N
38 C3' C2' C C sing 1.55 N N
39 C2' O2' C O sing 1.43 N N
40 C2' H2' C H sing 1.09 N N
41 O2' HO2' O H sing 0.97 N N
42 C4' C3' C C sing 1.54 N N
43 O3' C3' O C sing 1.43 N N
44 C3' H3' C H sing 1.09 N N
45 O3' HO3' O H sing 0.97 N N
46 O31 C32 O C sing 1.43 N N
47 C32 C33 C C sing 1.53 N N
48 C32 H32 C H sing 1.09 N N
49 C32 H32A C H sing 1.09 N N
50 C34 C33 C C sing 1.53 N N
51 C33 H33 C H sing 1.09 N N
52 C33 H33A C H sing 1.09 N N
53 C34 N35 C N sing 1.47 N N
54 C34 H34 C H sing 1.09 N N
55 C34 H34A C H sing 1.09 N N
56 N35 HN35 N H sing 1.01 N N
57 N35 HN3A N H sing 1.01 N N
58 O38 C36 O C doub 1.21 N N
59 C36 C37 C C sing 1.51 N N
60 C37 H37 C H sing 1.09 N N
61 C37 H37A C H sing 1.09 N N
62 C37 H37B C H sing 1.09 N N
63 C5' C4' C C sing 1.53 N N
64 C4' O4' C O sing 1.44 N N
65 C4' H4' C H sing 1.09 N N
66 C5' O5' C O sing 1.43 N N
67 C5' H5' C H sing 1.09 N N
68 C5' H5'A C H sing 1.09 N N
69 OD1 HOD1 O H sing 0.97 N N



7MC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
7MC 3r9g Open in New Window Bound ligand 2 1