Chemical Components in the PDB

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MTR : Summary

Code

MTR

One-letter code

T

Molecule name

(5-METHYL-6-OXO-1,6-DIHYDRO-PYRIDIN-3-YL)-1,2-DIDEOXY-RIBOFURANOSE-5-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R)-1,4-anhydro-2-deoxy-1-(5-methyl-6-oxo-1,6-dihydropyridin-3-yl)-5-O-phosphono-D-erythro-pentitol
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(5-methyl-6-oxo-1H-pyridin-3-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C11 H16 N O7 P

Formal charge

0

Molecular weight

305.221 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OCC2OC(C=1C=C(C(=O)NC=1)C)CC2O)(O)O
SMILES CACTVS 3.341 CC1=CC(=CNC1=O)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
SMILES OpenEye OEToolkits 1.5.0 CC1=CC(=CNC1=O)C2CC(C(O2)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 CC1=CC(=CNC1=O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=CC(=CNC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C11H16NO7P/c1-6-2-7(4-12-11(6)14)9-3-8(13)10(19-9)5-18-20(15,16)17/h2,4,8-10,13H,3,5H2,1H3,(H,12,14)(H2,15,16,17)/t8-,9+,10+/m0/s1

IUPAC InChI key

MUWYCJQCZPFLFI-IVZWLZJFSA-N
MTR

wwPDB Information

Atom count

36 (20 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DT

Defined at

2003-01-09

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



MTR : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 0.147 -0.857 -0.647
2 C1' C C1* R N N 0 1.516 -1.4 -0.86
3 C2 C C2 N N N 0 -0.9 -1.167 -1.425
4 C2' C C2* N N N 0 2.002 -2.267 0.293
5 C3' C C3* S N N 0 2.948 -3.218 -0.403
6 C4 C C4 N N N 0 -2.421 0.237 -0.148
7 C4' C C4* R N N 0 2.281 -3.431 -1.755
8 C5 C C5 N N N 0 -1.257 0.593 0.732
9 C5' C C5* N N N 0 1.303 -4.598 -1.754
10 C5M C C5M N N N 0 -1.504 1.536 1.865
11 C6 C C6 N N N 0 -0.056 0.054 0.462
12 H1' H H1* N N N 0 2.209 -0.57 -1.038
13 H2 H H2 N N N 0 -0.832 -1.838 -2.272
14 H2' H 1H2* N N N 0 2.476 -1.668 1.077
15 H2'' H 2H2* N N N 0 1.172 -2.831 0.737
16 H3 H H3 N N N 0 -2.903 -0.905 -1.804
17 H3' H H3* N N N 0 3.131 -4.142 0.152
18 H4' H H4* N N N 0 3.011 -3.566 -2.559
19 H5' H 1H5* N N N 0 0.512 -4.424 -1.024
20 H5'' H 2H5* N N N 0 1.825 -5.525 -1.514
21 H6 H H6 N N N 0 0.805 0.292 1.079
22 H71 H 1H5M N N N 0 -0.909 2.439 1.729
23 H72 H 2H5M N N N 0 -1.229 1.061 2.806
24 H73 H 3H5M N N N 0 -2.56 1.802 1.899
25 HO3' H H3T N N Y 0 4.684 -3.068 -1.253
26 HOP2 H 2HOP N N N 0 -2.25 -6.233 -2.129
27 HOP3 H 3HOP N N N 0 0.02 -8.091 -2.998
28 N3 N N3 N N N 0 -2.142 -0.639 -1.185
29 O3' O O3* N N N 0 4.199 -2.56 -0.584
30 O4 O O4 N N N 0 -3.539 0.705 0.058
31 O4' O O4* N N N 0 1.535 -2.229 -2.034
32 O5' O O5* N N N 0 0.729 -4.709 -3.045
33 OP1 O O1P N N N 0 -0.911 -5.928 -4.704
34 OP2 O O2P N N N 0 -1.446 -5.671 -2.136
35 OP3 O O3P N N Y 0 0.436 -7.216 -2.848
36 P P P N N N 0 -0.354 -5.883 -3.311



MTR : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP1 P O doub 1.5 N N
2 P OP2 P O sing 1.62 N N
3 P O5' P O sing 1.62 N N
4 P OP3 P O sing 1.62 N N
5 OP2 HOP2 O H sing 0.98 N N
6 O5' C5' O C sing 1.42 N N
7 C1 C6 C C sing 1.45 N N
8 C1 C2 C C doub 1.34 N N
9 C1 C1' C C sing 1.49 N N
10 C6 C5 C C doub 1.34 N N
11 C6 H6 C H sing 1.09 N N
12 C2 N3 C N sing 1.37 N N
13 C2 H2 C H sing 1.08 N N
14 N3 C4 N C sing 1.39 N N
15 N3 H3 N H sing 1.02 N N
16 C4 O4 C O doub 1.23 N N
17 C4 C5 C C sing 1.5 N N
18 C5 C5M C C sing 1.49 N N
19 C5M H71 C H sing 1.09 N N
20 C5M H72 C H sing 1.09 N N
21 C5M H73 C H sing 1.09 N N
22 C2' C1' C C sing 1.52 N N
23 C2' C3' C C sing 1.51 N N
24 C2' H2' C H sing 1.09 N N
25 C2' H2'' C H sing 1.1 N N
26 C5' C4' C C sing 1.52 N N
27 C5' H5' C H sing 1.09 N N
28 C5' H5'' C H sing 1.09 N N
29 C4' O4' C O sing 1.44 N N
30 C4' C3' C C sing 1.52 N N
31 C4' H4' C H sing 1.09 N N
32 O4' C1' O C sing 1.44 N N
33 C1' H1' C H sing 1.1 N N
34 C3' O3' C O sing 1.43 N N
35 C3' H3' C H sing 1.09 N N
36 O3' HO3' O H sing 0.97 N N
37 OP3 HOP3 O H sing 0.98 N N



MTR : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
MTR 1ngt Open in New Window Polymer component 2 1