Chemical Components in the PDB

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IPE : Summary

Code

IPE

One-letter code

X

Molecule name

3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

Synonyms

ISOPENTENYL PYROPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-methylbut-3-en-1-yl trihydrogen diphosphate
OpenEye OEToolkits 1.5.0 3-methylbut-3-enyl phosphono hydrogen phosphate

Formula

C5 H12 O7 P2

Formal charge

0

Molecular weight

246.092 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OP(=O)(O)O)(OCC\C(=C)C)O
SMILES CACTVS 3.341 CC(=C)CCO[P](O)(=O)O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(=C)CCOP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 CC(=C)CCO[P@](O)(=O)O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)

IUPAC InChI key

NUHSROFQTUXZQQ-UHFFFAOYSA-N
IPE

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

2005-03-16

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



IPE : 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 N N 0 2.133 -0.035 -0.129
2 O1 O O1 N N N 0 1.008 -0.127 -1.006
3 C2 C C2 N N N 0 3.417 -0.301 -0.917
4 C3 C C3 N N N 0 4.603 -0.203 0.007
5 C4 C C4 N N N 0 5.091 -1.284 0.563
6 C5 C C5 N N N 0 5.228 1.139 0.292
7 PA P PA R N N 0 -0.301 0.162 -0.115
8 O1A O O1A N N N 0 -0.33 -0.767 1.037
9 O2A O O2A N N N 0 -0.261 1.68 0.421
10 O3A O O3A N N N 0 -1.62 -0.055 -1.012
11 PB P PB N N N 0 -2.865 -0.147 0.004
12 O1B O O1B N N N 0 -3.299 1.336 0.457
13 O2B O O2B N N N 0 -2.472 -0.931 1.196
14 O3B O O3B N N N 0 -4.104 -0.868 -0.728
15 H11 H 1H1 N N N 0 2.035 -0.773 0.667
16 H12 H 2H1 N N N 0 2.174 0.964 0.305
17 H21 H 1H2 N N N 0 3.515 0.438 -1.713
18 H22 H 2H2 N N N 0 3.376 -1.299 -1.352
19 H41 H 1H4 N N N 0 5.942 -1.214 1.225
20 H42 H 2H4 N N N 0 4.644 -2.245 0.358
21 H51 H 1H5 N N N 0 6.066 1.011 0.977
22 H52 H 2H5 N N N 0 5.583 1.58 -0.639
23 H53 H 3H5 N N N 0 4.486 1.796 0.746
24 H2A H H2A N N N 0 -0.243 2.251 -0.358
25 H1B H H1B N N N 0 -3.547 1.813 -0.347
26 H3B H H3B N N N 0 -4.827 -0.903 -0.087



IPE : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 C2 C C sing 1.53 N N
3 C1 H11 C H sing 1.09 N N
4 C1 H12 C H sing 1.09 N N
5 O1 PA O P sing 1.61 N N
6 C2 C3 C C sing 1.51 N N
7 C2 H21 C H sing 1.09 N N
8 C2 H22 C H sing 1.09 N N
9 C3 C4 C C doub 1.31 N N
10 C3 C5 C C sing 1.51 N N
11 C4 H41 C H sing 1.08 N N
12 C4 H42 C H sing 1.08 N N
13 C5 H51 C H sing 1.09 N N
14 C5 H52 C H sing 1.09 N N
15 C5 H53 C H sing 1.09 N N
16 PA O1A P O doub 1.48 N N
17 PA O2A P O sing 1.61 N N
18 PA O3A P O sing 1.61 N N
19 O2A H2A O H sing 0.97 N N
20 O3A PB O P sing 1.61 N N
21 PB O1B P O sing 1.61 N N
22 PB O2B P O doub 1.48 N N
23 PB O3B P O sing 1.61 N N
24 O1B H1B O H sing 0.97 N N
25 O3B H3B O H sing 0.97 N N



IPE : Used in PDB Entries

Total Number of PDB Entries: 69
Ligand Code PDB Entry ID Type Total Distinct
IPE 1rqj Open in New Window Bound ligand 2 1
IPE 1x07 Open in New Window Bound ligand 1 1
IPE 1x08 Open in New Window Bound ligand 1 1
IPE 1x09 Open in New Window Bound ligand 2 1
IPE 1yhm Open in New Window Bound ligand 3 1
IPE 1zw5 Open in New Window Bound ligand 1 1
IPE 2e8t Open in New Window Bound ligand 2 1
IPE 2e8u Open in New Window Bound ligand 4 1
IPE 2e8w Open in New Window Bound ligand 3 1
IPE 2f8z Open in New Window Bound ligand 1 1
IPE 2uzh Open in New Window Bound ligand 1 1
IPE 2vg2 Open in New Window Bound ligand 2 1
IPE 2zev Open in New Window Bound ligand 1 1
IPE 2zry Open in New Window Bound ligand 4 1
IPE 3b05 Open in New Window Bound ligand 4 1
IPE 3ez3 Open in New Window Bound ligand 4 1
IPE 3iba Open in New Window Bound ligand 1 1
IPE 3ick Open in New Window Bound ligand 1 1
IPE 3icm Open in New Window Bound ligand 1 1
IPE 3icn Open in New Window Bound ligand 1 1
IPE 3icz Open in New Window Bound ligand 1 1
IPE 3k4y Open in New Window Bound ligand 2 1
IPE 3ke9 Open in New Window Bound ligand 2 1
IPE 3kem Open in New Window Bound ligand 2 1
IPE 3krc Open in New Window Bound ligand 2 1
IPE 3krf Open in New Window Bound ligand 1 1
IPE 3kro Open in New Window Bound ligand 2 1
IPE 3ldw Open in New Window Bound ligand 4 1
IPE 3ll5 Open in New Window Bound ligand 2 1
IPE 3oab Open in New Window Bound ligand 1 1
IPE 3oac Open in New Window Bound ligand 1 1
IPE 3wjo Open in New Window Bound ligand 2 1
IPE 4dwb Open in New Window Bound ligand 1 1
IPE 4dxj Open in New Window Bound ligand 3 1
IPE 4dzw Open in New Window Bound ligand 1 1
IPE 4e1e Open in New Window Bound ligand 1 1
IPE 4jkw Open in New Window Bound ligand 1 1
IPE 4jzb Open in New Window Bound ligand 2 1
IPE 4jzx Open in New Window Bound ligand 2 1
IPE 4kpd Open in New Window Bound ligand 1 1
IPE 4kqs Open in New Window Bound ligand 1 1
IPE 4kqu Open in New Window Bound ligand 1 1
IPE 4lfe Open in New Window Bound ligand 3 1
IPE 4lfg Open in New Window Bound ligand 4 1
IPE 4lls Open in New Window Bound ligand 2 1
IPE 4llt Open in New Window Bound ligand 4 1
IPE 4ng6 Open in New Window Bound ligand 1 1
IPE 4nke Open in New Window Bound ligand 1 1
IPE 4ogu Open in New Window Bound ligand 1 1
IPE 5cg6 Open in New Window Bound ligand 1 1
IPE 6b06 Open in New Window Bound ligand 3 1
IPE 6t7n Open in New Window Bound ligand 2 1
IPE 6w2l Open in New Window Bound ligand 2 1
IPE 7car Open in New Window Bound ligand 1 1
IPE 7lnu Open in New Window Bound ligand 1 1
IPE 7my0 Open in New Window Bound ligand 2 1
IPE 7my1 Open in New Window Bound ligand 1 1
IPE 7my6 Open in New Window Bound ligand 1 1
IPE 7pax Open in New Window Bound ligand 1 1
IPE 7s0m Open in New Window Bound ligand 2 1
IPE 8a6v Open in New Window Bound ligand 3 1
IPE 8a6z Open in New Window Bound ligand 12 1
IPE 8a7c Open in New Window Bound ligand 2 1
IPE 8a7j Open in New Window Bound ligand 2 1
IPE 8a7k Open in New Window Bound ligand 2 1
IPE 8f8k Open in New Window Bound ligand 1 1
IPE 8jya Open in New Window Bound ligand 1 1
IPE 8x35 Open in New Window Bound ligand 1 1
IPE 8x36 Open in New Window Bound ligand 2 1