Chemical Components in the PDB

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MVL : Summary

Code

MVL

One-letter code

X

Molecule name

(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL

Systematic names

ProgramVersionName
ACDLabs 12.01 (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol
OpenEye OEToolkits 1.7.6 (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol

Formula

C8 H12 N2 O4

Formal charge

0

Molecular weight

200.192 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1ccn2c1C(O)C(O)C(O)C2CO
SMILES CACTVS 3.385 OC[CH]1[CH](O)[CH](O)[CH](O)c2nccn12
SMILES OpenEye OEToolkits 1.7.6 c1cn2c(n1)C(C(C(C2CO)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@@H]1[C@@H](O)[C@H](O)[C@H](O)c2nccn12
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cn2c(n1)[C@H]([C@H]([C@@H]([C@H]2CO)O)O)O

IUPAC InChI

InChI=1S/C8H12N2O4/c11-3-4-5(12)6(13)7(14)8-9-1-2-10(4)8/h1-2,4-7,11-14H,3H2/t4-,5-,6+,7+/m1/s1

IUPAC InChI key

RZRDQZQPTISYKY-JWXFUTCRSA-N
MVL

wwPDB Information

Atom count

26 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-01-25

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



MVL : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 0.212 1.387 0.154
2 N10 N N10 N Y N 0 0.998 0.288 0.239
3 C3 C C3 S N N 0 -1.748 -0.043 0.601
4 C4 C C4 R N N 0 -0.953 -1.116 -0.16
5 C5 C C5 R N N 0 0.507 -1.09 0.306
6 C6 C C6 N N N 0 1.352 -1.981 -0.606
7 C7 C C7 N Y N 0 2.259 2.06 0.166
8 C8 C C8 N Y N 0 2.293 0.714 0.248
9 N1 N N1 N Y N 0 0.973 2.441 0.11
10 O3 O O3 N N N 0 -3.143 -0.205 0.338
11 O2 O O2 N N N 0 -1.76 1.568 -1.209
12 O4 O O4 N N Y 0 -1.517 -2.402 0.105
13 C2 C C2 R N N 0 -1.298 1.344 0.124
14 O6 O O6 N N N 0 2.691 -2.035 -0.112
15 H2 H H2 N N N 0 -1.701 2.11 0.787
16 H5 H H5 N N N 0 0.569 -1.45 1.333
17 H8 H H8 N N N 0 3.176 0.094 0.308
18 H3 H H3 N N N 0 -1.565 -0.145 1.671
19 H4 H H4 N N N 0 -0.999 -0.912 -1.229
20 HA H HA N N N 0 -3.705 0.441 0.787
21 HB H HB N N N 0 -2.442 -2.489 -0.163
22 H6C1 H H6C1 N N N 0 0.931 -2.986 -0.624
23 H6C2 H H6C2 N N N 0 1.353 -1.57 -1.616
24 H6 H H6 N N N 0 3.285 -2.583 -0.642
25 H7 H H7 N N N 0 3.117 2.716 0.149
26 HC H HC N N N 0 -1.494 2.421 -1.58



MVL : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N10 C N sing 1.35 N Y
2 C1 N1 C N doub 1.3 N Y
3 C1 C2 C C sing 1.51 N N
4 N10 C5 N C sing 1.46 N N
5 N10 C8 N C sing 1.36 N Y
6 C3 C4 C C sing 1.54 N N
7 C3 O3 C O sing 1.43 N N
8 C3 C2 C C sing 1.53 N N
9 C4 C5 C C sing 1.53 N N
10 C4 O4 C O sing 1.43 N N
11 C5 C6 C C sing 1.53 N N
12 C6 O6 C O sing 1.43 N N
13 C7 C8 C C doub 1.35 N Y
14 C7 N1 C N sing 1.34 N Y
15 O2 C2 O C sing 1.43 N N
16 C2 H2 C H sing 1.09 N N
17 C5 H5 C H sing 1.09 N N
18 C8 H8 C H sing 1.08 N N
19 C3 H3 C H sing 1.09 N N
20 C4 H4 C H sing 1.09 N N
21 O3 HA O H sing 0.97 N N
22 O4 HB O H sing 0.97 N N
23 C6 H6C1 C H sing 1.09 N N
24 C6 H6C2 C H sing 1.09 N N
25 O6 H6 O H sing 0.97 N N
26 C7 H7 C H sing 1.08 N N
27 O2 HC O H sing 0.97 N N



MVL : Used in PDB Entries

Total Number of PDB Entries: 13
Ligand Code PDB Entry ID Type Total Distinct
MVL 2vmf Open in New Window Bound ligand 2 1
MVL 2wzs Open in New Window Bound ligand 8 1
MVL 3d4y Open in New Window Bound ligand 1 1
MVL 4ayq Open in New Window Bound ligand 1 1
MVL 4cd5 Open in New Window Bound ligand 1 1
MVL 4cd8 Open in New Window Bound ligand 1 1
MVL 4re2 Open in New Window Bound ligand 1 1
MVL 6f90 Open in New Window Bound ligand 3 1
MVL 6f92 Open in New Window Bound ligand 4 1
MVL 6far Open in New Window Bound ligand 1 1
MVL 6rqk Open in New Window Bound ligand 4 1
MVL 6t7g Open in New Window Bound ligand 6 1
MVL 7nsn Open in New Window Bound ligand 3 1