Chemical Components in the PDB

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OOW : Summary

Code

OOW

One-letter code

X

Molecule name

{[(2R,3S,4R,5S,6R)-5-acetamido-3-hydroxy-4-(2-oxopropyl)-6-(phosphonooxy)oxan-2-yl]methoxy}phosphonic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(2~{R},3~{S},4~{R},5~{S},6~{R})-3-acetamido-5-oxidanyl-2-phosphonooxy-6-(phosphonooxymethyl)oxan-4-yl] ethanoate

Formula

C10 H19 N O13 P2

Formal charge

0

Molecular weight

423.204 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(=O)N[CH]1[CH](O[CH](CO[P](O)(O)=O)[CH](O)[CH]1OC(C)=O)O[P](O)(O)=O
SMILES OpenEye OEToolkits 2.0.7 CC(=O)NC1C(C(C(OC1OP(=O)(O)O)COP(=O)(O)O)O)OC(=O)C
Canonical SMILES CACTVS 3.385 CC(=O)N[C@@H]1[C@H](O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]1OC(C)=O)O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(=O)N[C@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)COP(=O)(O)O)O)OC(=O)C

IUPAC InChI

InChI=1S/C10H19NO13P2/c1-4(12)11-7-9(22-5(2)13)8(14)6(3-21-25(15,16)17)23-10(7)24-26(18,19)20/h6-10,14H,3H2,1-2H3,(H,11,12)(H2,15,16,17)(H2,18,19,20)/t6-,7+,8-,9-,10-/m1/s1

IUPAC InChI key

WZRFFNAOXAJBLK-JDDHQFAOSA-N
OOW

wwPDB Information

Atom count

45 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-03-25

Last modified at

2020-10-02

Status

Released

Obsoleted

Not Assigned



OOW : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O10 O O1 N N N 0 -4.501 1.549 -1.76
2 C26 C C1 N N N 0 -1.813 1.424 -0.17
3 C28 C C2 S N N 0 0.643 1.671 0.224
4 C27 C C3 R N N 0 -0.527 0.684 0.205
5 C29 C C4 R N N 0 1.935 0.912 0.54
6 C31 C C5 S N N 0 2.129 -0.199 -0.496
7 C32 C C6 R N N 0 0.901 -1.114 -0.487
8 C37 C C7 N N N 0 2.945 -0.281 -2.79
9 C39 C C8 N N N 0 3.109 0.329 -4.158
10 C40 C C9 N N N 0 3.39 2.453 1.63
11 C42 C C10 N N N 0 4.547 3.418 1.654
12 N34 N N1 N N N 0 2.288 0.394 -1.826
13 O19 O O2 N N N 0 -5.401 -0.315 -0.316
14 O20 O O3 N N N 0 -2.923 0.529 -0.075
15 O21 O O4 N N N 0 -4.915 2.072 0.674
16 O30 O O5 N N N 0 -0.269 -0.341 -0.758
17 O35 O O6 N N N 0 0.414 2.663 1.226
18 O36 O O7 N N N 0 3.061 1.828 0.489
19 O38 O O8 N N N 0 3.405 -1.379 -2.557
20 O41 O O9 N N N 0 2.758 2.242 2.639
21 P11 P P1 N N N 0 -4.437 0.971 -0.399
22 P P P2 N N N 0 0.125 -3.19 1.006
23 O1 O O10 N N N 0 -1.232 -3.213 0.415
24 O2 O O11 N N N 0 1.043 -4.299 0.285
25 O3 O O12 N N N 0 0.777 -1.733 0.795
26 O4 O O13 N N N 0 0.03 -3.513 2.58
27 H1 H H1 N N N 0 -1.962 2.261 0.511
28 H2 H H2 N N N 0 -1.733 1.796 -1.192
29 H3 H H3 N N N 0 0.731 2.15 -0.751
30 H4 H H4 N N N 0 -0.641 0.235 1.191
31 H5 H H5 N N N 0 1.866 0.474 1.536
32 H6 H H6 N N N 0 3.017 -0.78 -0.246
33 H7 H H7 N N N 0 1.015 -1.882 -1.252
34 H8 H H8 N N N 0 2.635 1.31 -4.178
35 H9 H H9 N N N 0 4.17 0.434 -4.385
36 H10 H H10 N N N 0 2.641 -0.316 -4.902
37 H11 H H11 N N N 0 4.357 4.231 0.954
38 H12 H H12 N N N 0 4.661 3.824 2.659
39 H13 H H13 N N N 0 5.46 2.897 1.367
40 H14 H H14 N N N 0 1.921 1.272 -2.013
41 H15 H H15 N N N 0 -6.331 -0.122 -0.5
42 H16 H H16 N N N 0 -4.899 1.762 1.589
43 H17 H H17 N N N 0 -0.392 3.18 1.091
44 H18 H H18 N N N 0 1.948 -4.34 0.623
45 H19 H H19 N N N 0 -0.355 -4.377 2.782



OOW : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O38 C37 O C doub 1.21 N N
2 O1 P O P doub 1.48 N N
3 C39 C37 C C sing 1.51 N N
4 C37 N34 C N sing 1.35 N N
5 P O2 P O sing 1.61 N N
6 P O4 P O sing 1.61 N N
7 P O3 P O sing 1.61 N N
8 O41 C40 O C doub 1.21 N N
9 N34 C31 N C sing 1.46 N N
10 C31 C32 C C sing 1.53 N N
11 C31 C29 C C sing 1.53 N N
12 C42 C40 C C sing 1.51 N N
13 C40 O36 C O sing 1.34 N N
14 C32 O3 C O sing 1.43 N N
15 C32 O30 C O sing 1.43 N N
16 O36 C29 O C sing 1.45 N N
17 C29 C28 C C sing 1.53 N N
18 O30 C27 O C sing 1.43 N N
19 C28 C27 C C sing 1.53 N N
20 C28 O35 C O sing 1.43 N N
21 C27 C26 C C sing 1.53 N N
22 C26 O20 C O sing 1.43 N N
23 O20 P11 O P sing 1.61 N N
24 O10 P11 O P doub 1.48 N N
25 P11 O21 P O sing 1.61 N N
26 P11 O19 P O sing 1.61 N N
27 C26 H1 C H sing 1.09 N N
28 C26 H2 C H sing 1.09 N N
29 C28 H3 C H sing 1.09 N N
30 C27 H4 C H sing 1.09 N N
31 C29 H5 C H sing 1.09 N N
32 C31 H6 C H sing 1.09 N N
33 C32 H7 C H sing 1.09 N N
34 C39 H8 C H sing 1.09 N N
35 C39 H9 C H sing 1.09 N N
36 C39 H10 C H sing 1.09 N N
37 C42 H11 C H sing 1.09 N N
38 C42 H12 C H sing 1.09 N N
39 C42 H13 C H sing 1.09 N N
40 N34 H14 N H sing 0.97 N N
41 O19 H15 O H sing 0.97 N N
42 O21 H16 O H sing 0.97 N N
43 O35 H17 O H sing 0.97 N N
44 O2 H18 O H sing 0.97 N N
45 O4 H19 O H sing 0.97 N N



OOW : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OOW 6y54 Open in New Window Bound ligand 3 1