Chemical Components in the PDB

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85Y : Summary

Code

85Y

One-letter code

U

Molecule name

2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},5~{R})-5-[5-(naphthalen-2-ylmethylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C21 H22 N3 O9 P

Formal charge

0

Molecular weight

491.388 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C3(N(C=C(C(=O)NCc2cc1ccccc1cc2)C(N3)=O)C4OC(C(C4)O)COP(O)(=O)O)=O
SMILES CACTVS 3.385 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3ccc4ccccc4c3)C(=O)NC2=O
SMILES OpenEye OEToolkits 2.0.6 c1ccc2cc(ccc2c1)CNC(=O)C3=CN(C(=O)NC3=O)C4CC(C(O4)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3ccc4ccccc4c3)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc2cc(ccc2c1)CNC(=O)C3=CN(C(=O)NC3=O)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C21H22N3O9P/c25-16-8-18(33-17(16)11-32-34(29,30)31)24-10-15(20(27)23-21(24)28)19(26)22-9-12-5-6-13-3-1-2-4-14(13)7-12/h1-7,10,16-18,25H,8-9,11H2,(H,22,26)(H,23,27,28)(H2,29,30,31)/t16-,17+,18+/m0/s1

IUPAC InChI key

OIDHQCJPEWHGIY-RCCFBDPRSA-N
85Y

wwPDB Information

Atom count

56 (34 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

U

Defined at

2017-01-06

Last modified at

2018-08-13

Status

Released

Obsoleted

Not Assigned



85Y : Atoms of Molecule

Total Number of Atoms: 56
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N N N 0 1.219 -0.593 -1.228
2 C20 C C2 N N N 0 -2.13 -0.994 1.288
3 C24 C C3 N Y N 0 -5.639 0.168 1.194
4 C30 C C4 N Y N 0 -8.521 -0.7 -0.93
5 C33 C C5 N Y N 0 -8.925 2.044 -0.58
6 C4 C C6 N N N 0 -1.073 -0.25 -0.923
7 C5 C C7 N N N 0 -0.955 -0.856 0.413
8 C23 C C8 N N N 0 -4.45 -0.495 1.84
9 C25 C C9 N Y N 0 -6.501 -0.578 0.45
10 C26 C C10 N Y N 0 -7.61 0.037 -0.154
11 O4 O O1 N N N 0 -2.147 0.154 -1.33
12 N3 N N1 N N N 0 0.036 -0.149 -1.685
13 O2 O O2 N N N 0 2.202 -0.483 -1.935
14 C6 C C11 N N N 0 0.289 -1.297 0.82
15 N1 N N2 N N N 0 1.352 -1.149 -0.013
16 C1' C C12 R N N 0 2.673 -1.607 0.424
17 O4' O O3 N N N 0 3.64 -0.542 0.302
18 C2' C C13 N N N 0 3.192 -2.721 -0.512
19 C3' C C14 S N N 0 4.709 -2.446 -0.617
20 O3' O O4 N N N 0 5.456 -3.554 -0.111
21 C4' C C15 R N N 0 4.926 -1.198 0.267
22 C5' C C16 N N N 0 5.977 -0.278 -0.359
23 O5' O O5 N N N 0 6.194 0.847 0.494
24 P P P1 N N N 0 7.238 2.023 0.147
25 OP3 O O6 N N Y 0 6.746 2.805 -1.171
26 OP2 O O7 N N N 0 7.318 3.051 1.383
27 O21 O O8 N N N 0 -2.036 -1.593 2.342
28 N22 N N3 N N N 0 -3.31 -0.456 0.921
29 C27 C C17 N Y N 0 -7.815 1.429 0.023
30 C28 C C18 N Y N 0 -6.904 2.166 0.799
31 C29 C C19 N Y N 0 -5.843 1.535 1.372
32 C31 C C20 N Y N 0 -9.585 -0.07 -1.499
33 C32 C C21 N Y N 0 -9.786 1.298 -1.325
34 H1 H H1 N N N 0 -8.378 -1.761 -1.074
35 H2 H H2 N N N 0 -9.094 3.103 -0.454
36 H3 H H3 N N N 0 -4.194 0.033 2.759
37 H4 H H4 N N N 0 -4.694 -1.531 2.072
38 H5 H H5 N N N 0 -6.332 -1.637 0.323
39 H6 H H6 N N N 0 -0.021 0.248 -2.569
40 H7 H H7 N N N 0 0.416 -1.751 1.791
41 H8 H H8 N N N 0 2.629 -1.963 1.453
42 H9 H H9 N N N 0 3.012 -3.703 -0.073
43 H10 H H10 N N N 0 2.721 -2.648 -1.492
44 H11 H H11 N N N 0 4.988 -2.236 -1.65
45 H12 H H12 N N N 0 5.31 -4.38 -0.593
46 H13 H H13 N N N 0 5.229 -1.493 1.271
47 H14 H H14 N N N 0 6.911 -0.826 -0.483
48 H15 H H15 N N N 0 5.625 0.066 -1.332
49 HOP3 H H16 N N Y 0 5.874 3.214 -1.084
50 HOP2 H H17 N N N 0 7.93 3.787 1.243
51 H18 H H18 N N N 0 -3.404 -0.043 0.048
52 H19 H H19 N N N 0 -7.048 3.227 0.942
53 H20 H H20 N N N 0 -5.144 2.104 1.968
54 H21 H H21 N N N 0 -10.283 -0.639 -2.095
55 H22 H H22 N N N 0 -10.639 1.773 -1.788
56 OP1 O O9 N N N 0 8.575 1.438 -0.097



85Y : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C32 C33 C C doub 1.36 N Y
2 C32 C31 C C sing 1.39 N Y
3 C33 C27 C C sing 1.4 N Y
4 C31 C30 C C doub 1.36 N Y
5 C27 C28 C C doub 1.41 N Y
6 C27 C26 C C sing 1.42 N Y
7 C30 C26 C C sing 1.41 N Y
8 C28 C29 C C sing 1.36 N Y
9 C26 C25 C C doub 1.4 N Y
10 C29 C24 C C doub 1.39 N Y
11 C25 C24 C C sing 1.36 N Y
12 C24 C23 C C sing 1.51 N N
13 C23 N22 C N sing 1.46 N N
14 N22 C20 N C sing 1.35 N N
15 C20 O21 C O doub 1.22 N N
16 C20 C5 C C sing 1.47 N N
17 O4 C4 O C doub 1.22 N N
18 C4 C5 C C sing 1.47 N N
19 C4 N3 C N sing 1.35 N N
20 C5 C6 C C doub 1.38 N N
21 N3 C2 N C sing 1.34 N N
22 C6 N1 C N sing 1.36 N N
23 C2 N1 C N sing 1.34 N N
24 C2 O2 C O doub 1.22 N N
25 N1 C1' N C sing 1.46 N N
26 C2' C1' C C sing 1.54 N N
27 C2' C3' C C sing 1.55 N N
28 C1' O4' C O sing 1.44 N N
29 O3' C3' O C sing 1.43 N N
30 C3' C4' C C sing 1.54 N N
31 O4' C4' O C sing 1.44 N N
32 C4' C5' C C sing 1.53 N N
33 O5' C5' O C sing 1.43 N N
34 O5' P O P sing 1.61 N N
35 OP2 P O P sing 1.61 N N
36 P OP3 P O sing 1.61 N N
37 C30 H1 C H sing 1.08 N N
38 C33 H2 C H sing 1.08 N N
39 C23 H3 C H sing 1.09 N N
40 C23 H4 C H sing 1.09 N N
41 C25 H5 C H sing 1.08 N N
42 N3 H6 N H sing 0.97 N N
43 C6 H7 C H sing 1.08 N N
44 C1' H8 C H sing 1.09 N N
45 C2' H9 C H sing 1.09 N N
46 C2' H10 C H sing 1.09 N N
47 C3' H11 C H sing 1.09 N N
48 O3' H12 O H sing 0.97 N N
49 C4' H13 C H sing 1.09 N N
50 C5' H14 C H sing 1.09 N N
51 C5' H15 C H sing 1.09 N N
52 OP3 HOP3 O H sing 0.97 N N
53 OP2 HOP2 O H sing 0.97 N N
54 N22 H18 N H sing 0.97 N N
55 C28 H19 C H sing 1.08 N N
56 C29 H20 C H sing 1.08 N N
57 C31 H21 C H sing 1.08 N N
58 C32 H22 C H sing 1.08 N N
59 P OP1 P O doub 1.48 N N



85Y : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
85Y 5uc6 Open in New Window Polymer component 7 7
85Y 7jtn Open in New Window Polymer component 14 7
85Y 7jtq Open in New Window Polymer component 14 7
85Y 7yq3 Open in New Window Polymer component 6 6
85Y 7yq4 Open in New Window Polymer component 3 3
85Y 7yq5 Open in New Window Polymer component 3 3
85Y 7yq6 Open in New Window Polymer component 6 3
85Y 8j1q Open in New Window Polymer component 22 22
85Y 8j26 Open in New Window Polymer component 19 19