Chemical Components in the PDB

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P4U : Summary

Code

P4U

One-letter code

U

Molecule name

4-propyl, uridine-5'-monophosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanylidene-4-propoxy-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C12 H19 N2 O9 P

Formal charge

0

Molecular weight

366.261 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCOC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 2.0.6 CCCOC1=NC(=O)N(C=C1)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.385 CCCOC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 2.0.6 CCCOC1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C12H19N2O9P/c1-2-5-21-8-3-4-14(12(17)13-8)11-10(16)9(15)7(23-11)6-22-24(18,19)20/h3-4,7,9-11,15-16H,2,5-6H2,1H3,(H2,18,19,20)/t7-,9-,10-,11-/m1/s1

IUPAC InChI key

YIPJYDZHQZNRLV-QCNRFFRDSA-N
P4U

wwPDB Information

Atom count

43 (24 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

U

Defined at

2017-09-25

Last modified at

2019-04-29

Status

Released

Obsoleted

Not Assigned



P4U : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1 R N N 0 -0.049 -1.828 0.596
2 C2 C C2 N N N 0 -1.675 -0.21 -0.214
3 C2' C C3 R N N 0 0.242 -2.469 -0.785
4 C3' C C4 S N N 0 1.79 -2.447 -0.832
5 C4 C C5 N N N 0 -3.831 -0.075 0.603
6 C4' C C6 R N N 0 2.184 -1.366 0.192
7 C5 C C7 N N N 0 -3.563 -1.143 1.48
8 C5' C C8 N N N 0 3.004 -0.272 -0.495
9 C6 C C9 N N N 0 -2.33 -1.707 1.472
10 N1 N N1 N N N 0 -1.386 -1.229 0.615
11 N3 N N2 N N N 0 -2.882 0.356 -0.213
12 O2 O O1 N N N 0 -0.818 0.206 -0.976
13 O2' O O2 N N N 0 -0.252 -3.809 -0.84
14 O3' O O3 N N N 0 2.319 -3.719 -0.451
15 O4 O O4 N N N 0 -5.05 0.507 0.594
16 O4' O O5 N N N 0 0.967 -0.809 0.72
17 O5' O O6 N N N 0 3.463 0.664 0.482
18 OP1 O O7 N N N 0 5.565 1.514 -0.627
19 OP2 O O8 N N N 0 3.5 2.955 -0.808
20 P P P1 N N N 0 4.358 1.95 0.112
21 C41 C C10 N N N 0 -5.248 1.584 -0.323
22 C42 C C11 N N N 0 -6.678 2.112 -0.189
23 C43 C C12 N N N 0 -6.89 3.266 -1.171
24 H1 H H1 N N N 0 0.051 -2.567 1.391
25 H2 H H2 N N N 0 -0.18 -1.867 -1.589
26 H3 H H3 N N N 0 2.137 -2.174 -1.829
27 H4 H H4 N N N 0 2.764 -1.814 0.999
28 H5 H H5 N N N 0 -4.327 -1.506 2.151
29 H6 H H6 N N N 0 3.86 -0.722 -0.998
30 H7 H H7 N N N 0 2.381 0.242 -1.227
31 H8 H H8 N N N 0 -2.101 -2.527 2.136
32 H9 H H9 N N N 0 -0.093 -4.252 -1.684
33 H14 H H14 N N N 0 -5.086 1.23 -1.341
34 H10 H H10 N N N 0 2.054 -4.445 -1.031
35 H12 H H12 N N N 0 2.693 3.281 -0.386
36 H13 H H13 N N N 0 -4.543 2.385 -0.1
37 H15 H H15 N N N 0 -7.383 1.311 -0.412
38 H16 H H16 N N N 0 -6.841 2.466 0.829
39 H17 H H17 N N N 0 -6.185 4.067 -0.948
40 H18 H H18 N N N 0 -6.728 2.911 -2.189
41 H19 H H19 N N N 0 -7.909 3.641 -1.076
42 OP3 O OP3 N N Y 0 4.8 2.704 1.464
43 H11 H H11 N N N 0 5.344 3.49 1.316



P4U : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP2 P O P sing 1.61 N N
2 O3' C3' O C sing 1.43 N N
3 C5' O5' C O sing 1.43 N N
4 C5' C4' C C sing 1.53 N N
5 O5' P O P sing 1.61 N N
6 C4' C3' C C sing 1.54 N N
7 C4' O4' C O sing 1.44 N N
8 P OP1 P O doub 1.48 N N
9 C3' C2' C C sing 1.55 N N
10 O2' C2' O C sing 1.43 N N
11 O4' C1' O C sing 1.44 N N
12 C2' C1' C C sing 1.55 N N
13 C1' N1 C N sing 1.47 N N
14 N1 C6 N C sing 1.36 N N
15 N1 C2 N C sing 1.35 N N
16 C6 C5 C C doub 1.36 N N
17 C5 C4 C C sing 1.41 N N
18 C2 O2 C O doub 1.22 N N
19 C2 N3 C N sing 1.33 N N
20 C4 N3 C N doub 1.32 N N
21 C4 O4 C O sing 1.35 N N
22 C41 O4 C O sing 1.43 N N
23 C41 C42 C C sing 1.53 N N
24 C42 C43 C C sing 1.53 N N
25 C1' H1 C H sing 1.09 N N
26 C2' H2 C H sing 1.09 N N
27 C3' H3 C H sing 1.09 N N
28 C4' H4 C H sing 1.09 N N
29 C5 H5 C H sing 1.08 N N
30 C5' H6 C H sing 1.09 N N
31 C5' H7 C H sing 1.09 N N
32 C6 H8 C H sing 1.08 N N
33 O2' H9 O H sing 0.97 N N
34 O3' H10 O H sing 0.97 N N
35 OP2 H12 O H sing 0.97 N N
36 C41 H13 C H sing 1.09 N N
37 C41 H14 C H sing 1.09 N N
38 C42 H15 C H sing 1.09 N N
39 C42 H16 C H sing 1.09 N N
40 C43 H17 C H sing 1.09 N N
41 C43 H18 C H sing 1.09 N N
42 C43 H19 C H sing 1.09 N N
43 P OP3 P O sing 1.61 N N
44 OP3 H11 O H sing 0.97 N N



P4U : Used in PDB Entries

Total Number of PDB Entries: 24
Ligand Code PDB Entry ID Type Total Distinct
P4U 6lqm Open in New Window Polymer component 1 1
P4U 6lsr Open in New Window Polymer component 1 1
P4U 6lss Open in New Window Polymer component 1 1
P4U 6lu8 Open in New Window Polymer component 1 1
P4U 6mtb Open in New Window Polymer component 1 1
P4U 6mtc Open in New Window Polymer component 1 1
P4U 6mtd Open in New Window Polymer component 1 1
P4U 6mte Open in New Window Polymer component 1 1
P4U 7oyd Open in New Window Polymer component 1 1
P4U 7ucj Open in New Window Polymer component 1 1
P4U 7uck Open in New Window Polymer component 1 1
P4U 8b5l Open in New Window Polymer component 1 1
P4U 8b6c Open in New Window Polymer component 1 1
P4U 8idt Open in New Window Polymer component 1 1
P4U 8idy Open in New Window Polymer component 1 1
P4U 8ie3 Open in New Window Polymer component 1 1
P4U 8ine Open in New Window Polymer component 1 1
P4U 8inf Open in New Window Polymer component 1 1
P4U 8ink Open in New Window Polymer component 1 1
P4U 8ipd Open in New Window Polymer component 1 1
P4U 8ipx Open in New Window Polymer component 1 1
P4U 8ipy Open in New Window Polymer component 1 1
P4U 8ir1 Open in New Window Polymer component 1 1
P4U 8ir3 Open in New Window Polymer component 1 1