Chemical Components in the PDB

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NWD : Summary

Code

NWD

One-letter code

A

Molecule name

3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine

Synonyms

nitrowillardiine

Systematic names

ProgramVersionName
ACDLabs 12.01 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
OpenEye OEToolkits 1.7.2 (2S)-2-azanyl-3-[5-nitro-2,4-bis(oxidanylidene)pyrimidin-1-yl]propanoic acid

Formula

C7 H8 N4 O6

Formal charge

0

Molecular weight

244.162 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CN1C=C(C(=O)NC1=O)[N+]([O-])=O
SMILES CACTVS 3.370 N[CH](CN1C=C(C(=O)NC1=O)[N+]([O-])=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.2 C1=C(C(=O)NC(=O)N1CC(C(=O)O)N)[N+](=O)[O-]
Canonical SMILES CACTVS 3.370 N[C@@H](CN1C=C(C(=O)NC1=O)[N+]([O-])=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.2 C1=C(C(=O)NC(=O)N1C[C@@H](C(=O)O)N)[N+](=O)[O-]

IUPAC InChI

InChI=1S/C7H8N4O6/c8-3(6(13)14)1-10-2-4(11(16)17)5(12)9-7(10)15/h2-3H,1,8H2,(H,13,14)(H,9,12,15)/t3-/m0/s1

IUPAC InChI key

IEBVITXSHAFLJR-VKHMYHEASA-N
NWD

wwPDB Information

Atom count

25 (17 without Hydrogen)

Polymer type

Amino Acid

Type description

L-peptide linking

Type code

ATOMP

Is modified

Yes

Standard parent

ALA

Defined at

2011-05-05

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



NWD : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -0.203 -0.228 -0.516
2 O1 O O1 N N N 0 2.831 2.551 -0.035
3 C2 C C2 N N N 0 0.092 -1.533 -0.381
4 N2 N N2 N N N 1 3.095 1.368 0.086
5 O2 O O2 N N N 0 -0.786 -2.364 -0.518
6 N3 N N3 N N N 0 1.345 -1.934 -0.096
7 O3 O O3 N N N -1 4.234 1.022 0.344
8 C4 C C4 N N N 0 2.329 -1.026 0.059
9 O4 O O4 N N N 0 3.464 -1.387 0.317
10 C5 C C5 N N N 0 2.033 0.352 -0.08
11 C6 C C6 N N N 0 0.767 0.725 -0.366
12 C7 C C7 N N N 0 -1.575 0.177 -0.832
13 C8 C C8 S N N 0 -2.355 0.396 0.466
14 N8 N N8 N N N 0 -2.278 -0.816 1.293
15 C9 C C9 N N N 0 -3.797 0.692 0.142
16 O91 O O91 N N N 0 -4.627 -0.181 0.229
17 O92 O O92 N N N 0 -4.158 1.926 -0.243
18 HN3 H HN3 N N N 0 1.54 -2.879 -0.002
19 H6 H H6 N N N 0 0.522 1.771 -0.476
20 H7 H H7 N N N 0 -1.557 1.104 -1.406
21 H7A H H7A N N N 0 -2.058 -0.604 -1.419
22 H8 H H8 N N N 0 -1.925 1.236 1.011
23 HN8 H HN8 N N N 0 -2.671 -1.61 0.809
24 HN8A H HN8A N N N 0 -1.327 -1.0 1.577
25 H81 H H81 N N N 0 -5.094 2.068 -0.44



NWD : 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 N1 C2 N C sing 1.34 N N
2 N1 C6 N C sing 1.37 N N
3 N1 C7 N C sing 1.47 N N
4 O1 N2 O N doub 1.22 N N
5 C2 O2 C O doub 1.22 N N
6 C2 N3 C N sing 1.35 N N
7 N2 O3 N O sing 1.22 N N
8 N2 C5 N C sing 1.48 N N
9 N3 C4 N C sing 1.35 N N
10 N3 HN3 N H sing 0.97 N N
11 C4 O4 C O doub 1.22 N N
12 C4 C5 C C sing 1.42 N N
13 C5 C6 C C doub 1.35 N N
14 C6 H6 C H sing 1.08 N N
15 C7 C8 C C sing 1.53 N N
16 C7 H7 C H sing 1.09 N N
17 C7 H7A C H sing 1.09 N N
18 C8 N8 C N sing 1.47 N N
19 C8 C9 C C sing 1.51 N N
20 C8 H8 C H sing 1.09 N N
21 N8 HN8 N H sing 1.01 N N
22 N8 HN8A N H sing 1.01 N N
23 C9 O91 C O doub 1.21 N N
24 C9 O92 C O sing 1.34 N N
25 O92 H81 O H sing 0.97 N N



NWD : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
NWD 3rtw Open in New Window Bound ligand 3 1
NWD 4q30 Open in New Window Bound ligand 3 1
NWD 4u4f Open in New Window Bound ligand 4 1