Chemical Components in the PDB

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MBZ : Summary

Code

MBZ

One-letter code

N

Molecule name

1-[2-DEOXYRIBOFURANOSYL]-4-METHYL-BENZOIMIDAZOLE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methyl-1H-benzimidazole
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(4-methylbenzimidazol-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C13 H17 N2 O6 P

Formal charge

0

Molecular weight

328.258 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1c(cccc12)C)CC3O
SMILES CACTVS 3.341 Cc1cccc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.5.0 Cc1cccc2c1ncn2C3CC(C(O3)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 Cc1cccc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1cccc2c1ncn2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C13H17N2O6P/c1-8-3-2-4-9-13(8)14-7-15(9)12-5-10(16)11(21-12)6-20-22(17,18)19/h2-4,7,10-12,16H,5-6H2,1H3,(H2,17,18,19)/t10-,11+,12+/m0/s1

IUPAC InChI key

ZNNQATJVEJKFID-QJPTWQEYSA-N
MBZ

wwPDB Information

Atom count

39 (22 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

HETAIN

Is modified

Yes

Standard parent

Not Assigned

Defined at

2000-02-03

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



MBZ : 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 P P P N N N 0 0.934 -0.167 -4.6
2 OP1 O O1P N N N 0 1.795 0.973 -4.217
3 OP2 O O2P N N N 0 1.83 -1.304 -5.304
4 OP3 O O3P N N Y 0 -0.198 0.336 -5.628
5 O5' O O5* N N N 0 0.232 -0.774 -3.284
6 O3' O O3* N N N 0 -3.397 0.936 -1.382
7 C1' C C1* R N N 0 -0.972 -0.537 0.833
8 C2' C C2* N N N 0 -2.167 0.422 0.677
9 C3' C C3* S N N 0 -2.093 0.883 -0.798
10 C4' C C4* R N N 0 -1.241 -0.237 -1.446
11 C5' C C5* N N N 0 -0.544 0.276 -2.707
12 O4' O O4* N N N 0 -0.274 -0.563 -0.422
13 C5M C C5M N N N 0 2.221 0.934 5.904
14 C6 C C6 N Y N 0 1.097 0.194 5.227
15 C7 C C7 N Y N 0 0.902 0.326 3.85
16 N7 N N7 N Y N 0 1.546 1.017 2.875
17 C8 C C8 N Y N 0 0.97 0.798 1.729
18 N1 N N1 N Y N 0 -0.079 -0.052 1.889
19 C9 C C9 N Y N 0 -0.146 -0.374 3.229
20 C10 C C10 N Y N 0 -0.983 -1.179 3.989
21 C11 C C11 N Y N 0 -0.775 -1.29 5.348
22 C12 C C12 N Y N 0 0.263 -0.602 5.959
23 HOP2 H 2HOP N N N 0 2.232 -0.899 -6.085
24 HOP3 H 3HOP N N N 0 -0.735 -0.435 -5.851
25 HO'3 H 3HO* N N N 0 -3.903 1.586 -0.875
26 H1' H H1* N N N 0 -1.329 -1.536 1.08
27 H2' H 1H2* N N N 0 -3.104 -0.101 0.867
28 H2'' H 2H2* N N N 0 -2.063 1.274 1.349
29 H3' H H3* N N N 0 -1.593 1.848 -0.88
30 H4' H H4* N N N 0 -1.86 -1.104 -1.677
31 H5' H 1H5* N N N 0 -1.293 0.611 -3.426
32 H5'' H 2H5* N N N 0 0.107 1.11 -2.448
33 H71 H 1H5M N N N 0 3.116 0.312 5.907
34 H72 H 2H5M N N N 0 2.424 1.859 5.365
35 H73 H 3H5M N N N 0 1.937 1.166 6.931
36 H8 H H8 N N N 0 1.281 1.228 0.788
37 H10 H H10 N N N 0 -1.793 -1.716 3.519
38 H11 H H11 N N N 0 -1.425 -1.916 5.941
39 H12 H H12 N N N 0 0.414 -0.699 7.024



MBZ : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP1 P O doub 1.48 N N
2 P OP2 P O sing 1.61 N N
3 P OP3 P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 OP2 HOP2 O H sing 0.97 N N
6 OP3 HOP3 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 O3' C3' O C sing 1.43 N N
9 O3' HO'3 O H sing 0.97 N N
10 C1' C2' C C sing 1.54 N N
11 C1' O4' C O sing 1.44 N N
12 C1' N1 C N sing 1.47 N N
13 C1' H1' C H sing 1.09 N N
14 C2' C3' C C sing 1.55 N N
15 C2' H2' C H sing 1.09 N N
16 C2' H2'' C H sing 1.09 N N
17 C3' C4' C C sing 1.55 N N
18 C3' H3' C H sing 1.09 N N
19 C4' C5' C C sing 1.53 N N
20 C4' O4' C O sing 1.45 N N
21 C4' H4' C H sing 1.09 N N
22 C5' H5' C H sing 1.09 N N
23 C5' H5'' C H sing 1.09 N N
24 C5M C6 C C sing 1.51 N N
25 C5M H71 C H sing 1.09 N N
26 C5M H72 C H sing 1.09 N N
27 C5M H73 C H sing 1.09 N N
28 C6 C7 C C sing 1.4 N Y
29 C6 C12 C C doub 1.37 N Y
30 C7 N7 C N sing 1.36 N Y
31 C7 C9 C C doub 1.4 N Y
32 N7 C8 N C doub 1.3 N Y
33 C8 N1 C N sing 1.36 N Y
34 C8 H8 C H sing 1.08 N N
35 N1 C9 N C sing 1.38 N Y
36 C9 C10 C C sing 1.39 N Y
37 C10 C11 C C doub 1.38 N Y
38 C10 H10 C H sing 1.08 N N
39 C11 C12 C C sing 1.39 N Y
40 C11 H11 C H sing 1.08 N N
41 C12 H12 C H sing 1.08 N N



MBZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
MBZ 1eek Open in New Window Polymer component 1 1