Chemical Components in the PDB

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H2B : Summary

Code

H2B

One-letter code

X

Molecule name

2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE

Synonyms

QUINONOID 7,8-TETRAHYDROBIOPTERIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (6R)-2-amino-6-[(1R,2S)-1,2-dihydroxypropyl]-7,8-dihydropteridin-4(6H)-one
OpenEye OEToolkits 1.5.0 (6R)-2-amino-6-[(1R,2S)-1,2-dihydroxypropyl]-7,8-dihydro-6H-pteridin-4-one

Formula

C9 H13 N5 O3

Formal charge

0

Molecular weight

239.231 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(N=C2NCC(N=C12)C(O)C(O)C)N
SMILES CACTVS 3.341 C[CH](O)[CH](O)[CH]1CNC2=NC(=NC(=O)C2=N1)N
SMILES OpenEye OEToolkits 1.5.0 CC(C(C1CNC2=NC(=NC(=O)C2=N1)N)O)O
Canonical SMILES CACTVS 3.341 C[C@H](O)[C@H](O)[C@H]1CNC2=NC(=NC(=O)C2=N1)N
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@H]([C@@H]([C@H]1CNC2=NC(=NC(=O)C2=N1)N)O)O

IUPAC InChI

InChI=1S/C9H13N5O3/c1-3(15)6(16)4-2-11-7-5(12-4)8(17)14-9(10)13-7/h3-4,6,15-16H,2H2,1H3,(H3,10,11,13,14,17)/t3-,4+,6-/m0/s1

IUPAC InChI key

ZHQJVZLJDXWFFX-RPDRRWSUSA-N
H2B

wwPDB Information

Atom count

30 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-12-16

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



H2B : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -1.142 -0.046 -2.792
2 C2 C C2 N N N 0 -0.037 0.048 -3.536
3 N2 N N2 N N N 0 -0.189 0.096 -4.898
4 N3 N N3 N N N 0 1.19 0.098 -3.054
5 C4 C C4 N N N 0 1.438 0.04 -1.738
6 O4 O O4 N N N 0 2.573 0.092 -1.301
7 C4A C C4A N N N 0 0.259 -0.088 -0.834
8 C8A C C8A N N N 0 -1.079 -0.104 -1.483
9 N5 N N5 N N N 0 0.373 -0.176 0.442
10 N8 N N8 N N N 0 -2.185 -0.174 -0.683
11 C6 C C6 R N N 0 -0.79 -0.339 1.314
12 C7 C C7 N N N 0 -2.025 0.321 0.697
13 C9 C C9 R N N 0 -0.498 0.305 2.67
14 O9 O O9 N N N 0 -1.626 0.137 3.53
15 C10 C C10 S N N 0 0.727 -0.361 3.298
16 C11 C C11 N N N 0 1.019 0.283 4.655
17 O10 O O10 N N N 0 1.855 -0.192 2.438
18 H22 H 2H2 N N N 0 0.59 0.165 -5.471
19 H21 H 1H2 N N N 0 -1.076 0.062 -5.289
20 H8 H H8 N N N 0 -3.028 -0.53 -1.004
21 H6 H H6 N N N 0 -0.985 -1.402 1.456
22 H71 H 1H7 N N N 0 -2.908 0.065 1.282
23 H72 H 2H7 N N N 0 -1.893 1.403 0.684
24 H9 H H9 N N N 0 -0.302 1.368 2.532
25 H9O1 H 1H9O N N N 0 -1.765 -0.815 3.626
26 H10 H H10 N N N 0 0.531 -1.424 3.436
27 H113 H 3H11 N N N 0 1.892 -0.191 5.102
28 H112 H 2H11 N N N 0 1.215 1.347 4.516
29 H1O1 H 1H1O N N N 0 1.994 0.759 2.342
30 H111 H 1H11 N N N 0 0.158 0.155 5.311



H2B : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.34 N N
2 N1 C8A N C doub 1.31 N N
3 C2 N2 C N sing 1.37 N N
4 C2 N3 C N doub 1.32 N N
5 N2 H22 N H sing 0.97 N N
6 N2 H21 N H sing 0.97 N N
7 N3 C4 N C sing 1.34 N N
8 C4 O4 C O doub 1.22 N N
9 C4 C4A C C sing 1.49 N N
10 C4A C8A C C sing 1.49 N N
11 C4A N5 C N doub 1.28 N N
12 C8A N8 C N sing 1.37 N N
13 N5 C6 N C sing 1.46 N N
14 N8 C7 N C sing 1.47 N N
15 N8 H8 N H sing 0.97 N N
16 C6 C7 C C sing 1.53 N N
17 C6 C9 C C sing 1.53 N N
18 C6 H6 C H sing 1.09 N N
19 C7 H71 C H sing 1.09 N N
20 C7 H72 C H sing 1.09 N N
21 C9 O9 C O sing 1.43 N N
22 C9 C10 C C sing 1.53 N N
23 C9 H9 C H sing 1.09 N N
24 O9 H9O1 O H sing 0.97 N N
25 C10 C11 C C sing 1.53 N N
26 C10 O10 C O sing 1.43 N N
27 C10 H10 C H sing 1.09 N N
28 C11 H113 C H sing 1.09 N N
29 C11 H112 C H sing 1.09 N N
30 C11 H111 C H sing 1.09 N N
31 O10 H1O1 O H sing 0.97 N N



H2B : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
H2B 1dww Open in New Window Bound ligand 2 1
H2B 1tg2 Open in New Window Bound ligand 1 1
H2B 2fbz Open in New Window Bound ligand 1 1
H2B 2v6t Open in New Window Bound ligand 2 1
H2B 4cx1 Open in New Window Bound ligand 2 1
H2B 4cx2 Open in New Window Bound ligand 2 1
H2B 4nos Open in New Window Bound ligand 1 1