Chemical Components in the PDB

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NPJ : Summary

Code

NPJ

One-letter code

X

Molecule name

4-NITROPHENYL 4-O-ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GALACTOPYRANOSIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 4-nitrophenyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
OpenEye OEToolkits 1.5.0 (2R,3R,4S,5S,6R)-2-[(2R,3S,4R,5R,6R)-4,5-dihydroxy-2-(hydroxymethyl)-6-(4-nitrophenoxy)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol

Formula

C18 H25 N O13

Formal charge

0

Molecular weight

463.39 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 [O-][N+](=O)c3ccc(OC2OC(C(OC1OC(CO)C(O)C(O)C1O)C(O)C2O)CO)cc3
SMILES CACTVS 3.341 OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](O[CH]2CO)Oc3ccc(cc3)[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)OC3C(C(C(C(O3)CO)O)O)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](O[C@@H]2CO)Oc3ccc(cc3)[N+]([O-])=O)[C@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[N+](=O)[O-])O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O

IUPAC InChI

InChI=1S/C18H25NO13/c20-5-9-11(22)12(23)14(25)18(30-9)32-16-10(6-21)31-17(15(26)13(16)24)29-8-3-1-7(2-4-8)19(27)28/h1-4,9-18,20-26H,5-6H2/t9-,10-,11-,12+,13-,14-,15-,16-,17+,18-/m1/s1

IUPAC InChI key

IAYJZWFYUSNIPN-LTHBGAKLSA-N
NPJ

wwPDB Information

Atom count

57 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-04-07

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



NPJ : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1A C C1A R N N 0 -3.342 -0.859 0.065
2 C2A C C2A R N N 0 -4.374 -0.808 -1.064
3 C3A C C3A S N N 0 -4.462 0.627 -1.596
4 C4A C C4A S N N 0 -4.735 1.57 -0.418
5 C5A C C5A R N N 0 -3.674 1.34 0.661
6 C6A C C6A N N N 0 -3.917 2.302 1.826
7 O1A O O1A N N N 0 -2.074 -0.426 -0.433
8 O2A O O2A N N N 0 -3.975 -1.687 -2.117
9 O3A O O3A N N N 0 -5.525 0.722 -2.546
10 O4A O O4A N N N 0 -4.674 2.925 -0.867
11 O5A O O5A N N N 0 -3.749 -0.004 1.132
12 O6A O O6A N N N 0 -2.86 2.172 2.779
13 C1B C C1B R N N 0 1.592 -1.624 1.012
14 C2B C C2B R N N 0 0.472 -2.653 1.186
15 C6B C C6B N N N 0 -0.255 1.518 0.635
16 C3B C C3B R N N 0 -0.691 -2.288 0.256
17 C4B C C4B S N N 0 -1.094 -0.833 0.523
18 C5B C C5B R N N 0 0.143 0.059 0.401
19 O1B O O1B N N N 0 2.019 -1.613 -0.352
20 O2B O O2B N N N 0 0.96 -3.954 0.853
21 O3B O O3B N N N 0 -1.802 -3.148 0.513
22 O5B O O5B N N N 0 1.116 -0.328 1.369
23 O6B O O6B N N N 0 0.877 2.362 0.415
24 C1C C C1C N Y N 0 5.479 0.628 -0.5
25 C2C C C2C N Y N 0 4.84 0.424 0.709
26 C3C C C3C N Y N 0 3.681 -0.326 0.761
27 C4C C C4C N Y N 0 3.158 -0.875 -0.401
28 C5C C C5C N Y N 0 3.804 -0.673 -1.612
29 C6C C C6C N Y N 0 4.96 0.082 -1.66
30 N1C N N1C N N N 1 6.72 1.433 -0.553
31 O2C O O2C N N N -1 7.178 1.914 0.467
32 H3A H H3A N N N 0 -3.52 0.899 -2.072
33 O3C O O3C N N N 0 7.284 1.613 -1.618
34 H1A H H1A N N N 0 -3.257 -1.881 0.432
35 H2A H H2A N N N 0 -5.348 -1.115 -0.681
36 H4A H H4A N N N 0 -5.724 1.365 -0.009
37 H5A H H5A N N N 0 -2.685 1.522 0.241
38 H6A1 H 1H6A N N N 0 -4.867 2.062 2.302
39 H6A2 H 2H6A N N N 0 -3.946 3.325 1.452
40 HO2A H HO2A N N N 0 -3.927 -2.574 -1.737
41 HO3A H HO3A N N N 0 -5.317 0.104 -3.261
42 HO4A H HO4A N N N 0 -5.352 3.024 -1.549
43 HO6A H HO6A N N N 0 -3.051 2.793 3.494
44 H1B H H1B N N N 0 2.432 -1.891 1.652
45 H2B H H2B N N N 0 0.128 -2.646 2.22
46 H3B H H3B N N N 0 -0.377 -2.396 -0.782
47 H4B H H4B N N N 0 -1.507 -0.748 1.528
48 H5B H H5B N N N 0 0.565 -0.045 -0.599
49 H6B1 H 1H6B N N N 0 -1.052 1.792 -0.055
50 H6B2 H 2H6B N N N 0 -0.604 1.639 1.661
51 HO2B H HO2B N N N 0 1.689 -4.144 1.46
52 HO3B H HO3B N N N 0 -1.505 -4.051 0.333
53 HO6B H HO6B N N N 0 0.584 3.27 0.573
54 H2C H H2C N N N 0 5.248 0.851 1.613
55 H3C H H3C N N N 0 3.182 -0.485 1.706
56 H5C H H5C N N N 0 3.399 -1.099 -2.518
57 H6C H H6C N N N 0 5.461 0.244 -2.603



NPJ : 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 C1A C2A C C sing 1.53 N N
2 C1A O1A C O sing 1.43 N N
3 C1A O5A C O sing 1.43 N N
4 C1A H1A C H sing 1.09 N N
5 C2A C3A C C sing 1.53 N N
6 C2A O2A C O sing 1.43 N N
7 C2A H2A C H sing 1.09 N N
8 C3A C4A C C sing 1.53 N N
9 C3A O3A C O sing 1.43 N N
10 C3A H3A C H sing 1.09 N N
11 C4A C5A C C sing 1.53 N N
12 C4A O4A C O sing 1.43 N N
13 C4A H4A C H sing 1.09 N N
14 C5A C6A C C sing 1.53 N N
15 C5A O5A C O sing 1.43 N N
16 C5A H5A C H sing 1.09 N N
17 C6A O6A C O sing 1.43 N N
18 C6A H6A1 C H sing 1.09 N N
19 C6A H6A2 C H sing 1.09 N N
20 O1A C4B O C sing 1.43 N N
21 O2A HO2A O H sing 0.97 N N
22 O3A HO3A O H sing 0.97 N N
23 O4A HO4A O H sing 0.97 N N
24 O6A HO6A O H sing 0.97 N N
25 C1B C2B C C sing 1.53 N N
26 C1B O1B C O sing 1.43 N N
27 C1B O5B C O sing 1.43 N N
28 C1B H1B C H sing 1.09 N N
29 C2B C3B C C sing 1.53 N N
30 C2B O2B C O sing 1.43 N N
31 C2B H2B C H sing 1.09 N N
32 C3B C4B C C sing 1.53 N N
33 C3B O3B C O sing 1.43 N N
34 C3B H3B C H sing 1.09 N N
35 C4B C5B C C sing 1.53 N N
36 C4B H4B C H sing 1.09 N N
37 C5B C6B C C sing 1.53 N N
38 C5B O5B C O sing 1.43 N N
39 C5B H5B C H sing 1.09 N N
40 C6B O6B C O sing 1.43 N N
41 C6B H6B1 C H sing 1.09 N N
42 C6B H6B2 C H sing 1.09 N N
43 O1B C4C O C sing 1.36 N N
44 O2B HO2B O H sing 0.97 N N
45 O3B HO3B O H sing 0.97 N N
46 O6B HO6B O H sing 0.97 N N
47 C1C C2C C C doub 1.38 N Y
48 C1C C6C C C sing 1.38 N Y
49 C1C N1C C N sing 1.48 N N
50 C2C C3C C C sing 1.38 N Y
51 C2C H2C C H sing 1.08 N N
52 C3C C4C C C doub 1.39 N Y
53 C3C H3C C H sing 1.08 N N
54 C4C C5C C C sing 1.39 N Y
55 C5C C6C C C doub 1.38 N Y
56 C5C H5C C H sing 1.08 N N
57 C6C H6C C H sing 1.08 N N
58 N1C O2C N O sing 1.22 N N
59 N1C O3C N O doub 1.22 N N



NPJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NPJ 2ggx Open in New Window Bound ligand 3 1