Chemical Components in the PDB

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IP8 : Summary

Code

IP8

One-letter code

X

Molecule name

Isopentenyl phosphate

Synonyms

3-methylbut-3-en-1-yl dihydrogen phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 3-methylbut-3-en-1-yl dihydrogen phosphate
OpenEye OEToolkits 1.7.6 3-methylbut-3-enyl dihydrogen phosphate

Formula

C5 H11 O4 P

Formal charge

0

Molecular weight

166.112 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(OCCC(=C)\C)(O)O
SMILES CACTVS 3.370 CC(=C)CCO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(=C)CCOP(=O)(O)O
Canonical SMILES CACTVS 3.370 CC(=C)CCO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(=C)CCOP(=O)(O)O

IUPAC InChI

InChI=1S/C5H11O4P/c1-5(2)3-4-9-10(6,7)8/h1,3-4H2,2H3,(H2,6,7,8)

IUPAC InChI key

QMZRXYCCCYYMHF-UHFFFAOYSA-N
IP8

wwPDB Information

Atom count

21 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-10-21

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



IP8 : Atoms of Molecule

Total Number of Atoms: 21
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O O O N N N 0 2.023 -0.892 -1.252
2 C1 C C1 N N N 0 -0.751 -0.025 -0.102
3 O1 O O1 N N N 0 0.472 -0.2 0.616
4 P1 P P1 N N N 0 1.921 -0.016 -0.063
5 C2 C C2 N N N 0 -1.933 -0.273 0.837
6 O2 O O2 N N N 0 3.065 -0.416 0.997
7 C3 C C3 N N N 0 -3.223 -0.089 0.081
8 O3 O O3 N N Y 0 2.115 1.519 -0.509
9 C4 C C4 N N N 0 -3.818 1.288 -0.07
10 C5 C C5 N N N 0 -3.827 -1.125 -0.446
11 H1 H H1 N N N 0 -0.802 0.992 -0.49
12 H1A H H1A N N N 0 -0.79 -0.732 -0.93
13 H2 H H2 N N N 0 -1.881 -1.29 1.225
14 H2A H H2A N N N 0 -1.893 0.435 1.666
15 HO2 H HO2 N N N 0 3.965 -0.329 0.656
16 HO3 H HO3 N N Y 0 2.06 2.15 0.222
17 H4 H H4 N N N 0 -3.18 2.016 0.43
18 H4A H H4A N N N 0 -3.894 1.537 -1.129
19 H4B H H4B N N N 0 -4.811 1.306 0.379
20 H5 H H5 N N N 0 -4.752 -0.993 -0.988
21 H5A H H5A N N N 0 -3.401 -2.111 -0.338



IP8 : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O P1 O P doub 1.48 N N
2 C1 C2 C C sing 1.53 N N
3 C1 O1 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C1 H1A C H sing 1.09 N N
6 P1 O1 P O sing 1.61 N N
7 O3 P1 O P sing 1.61 N N
8 P1 O2 P O sing 1.61 N N
9 C3 C2 C C sing 1.51 N N
10 C2 H2 C H sing 1.09 N N
11 C2 H2A C H sing 1.09 N N
12 O2 HO2 O H sing 0.97 N N
13 C5 C3 C C doub 1.31 N N
14 C3 C4 C C sing 1.51 N N
15 O3 HO3 O H sing 0.97 N N
16 C4 H4 C H sing 1.09 N N
17 C4 H4A C H sing 1.09 N N
18 C4 H4B C H sing 1.09 N N
19 C5 H5 C H sing 1.08 N N
20 C5 H5A C H sing 1.08 N N



IP8 : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
IP8 3k52 Open in New Window Bound ligand 2 1
IP8 3lkk Open in New Window Bound ligand 2 1
IP8 3ll5 Open in New Window Bound ligand 2 1
IP8 4ar8 Open in New Window Polymer component 2 1
IP8 4arf Open in New Window Polymer component 1 1
IP8 6qlh Open in New Window Bound ligand 1 1