Chemical Components in the PDB

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NDF : Summary

Code

NDF

One-letter code

F

Molecule name

N-(CARBOXYCARBONYL)-D-PHENYLALANINE

Systematic names

ProgramVersionName
ACDLabs 10.04 N-(carboxycarbonyl)-D-phenylalanine
OpenEye OEToolkits 1.5.0 (2R)-2-(carboxycarbonylamino)-3-phenyl-propanoic acid

Formula

C11 H11 N O5

Formal charge

0

Molecular weight

237.209 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(=O)NC(C(=O)O)Cc1ccccc1
SMILES CACTVS 3.341 OC(=O)[CH](Cc1ccccc1)NC(=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)CC(C(=O)O)NC(=O)C(=O)O
Canonical SMILES CACTVS 3.341 OC(=O)[C@@H](Cc1ccccc1)NC(=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)C[C@H](C(=O)O)NC(=O)C(=O)O

IUPAC InChI

InChI=1S/C11H11NO5/c13-9(11(16)17)12-8(10(14)15)6-7-4-2-1-3-5-7/h1-5,8H,6H2,(H,12,13)(H,14,15)(H,16,17)/t8-/m1/s1

IUPAC InChI key

ULQWGBCNOHBNDB-MRVPVSSYSA-N
NDF

wwPDB Information

Atom count

28 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

D-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

PHE

Defined at

2004-12-26

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NDF : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CD1 C CD1 N Y N 0 0.791 -0.828 2.805
2 CE1 C CE1 N Y N 0 -0.158 -1.067 3.781
3 CZ C CZ N Y N 0 -1.231 -0.208 3.926
4 CE2 C CE2 N Y N 0 -1.355 0.889 3.096
5 CD2 C CD2 N Y N 0 -0.403 1.131 2.123
6 CG C CG N Y N 0 0.667 0.269 1.974
7 CB C CB N N N 0 1.702 0.53 0.911
8 CA C CA R N N 0 1.292 -0.173 -0.383
9 C C C N N N 0 2.327 0.087 -1.447
10 O O O N N N 0 3.265 -0.663 -1.573
11 OXT O OXT N N Y 0 2.206 1.153 -2.253
12 N N N N N N 0 -0.0050 0.339 -0.828
13 C2 C C2 N N N 0 -0.843 -0.457 -1.521
14 O2' O O2' N N N 0 -0.523 -1.599 -1.776
15 C1 C C1 N N N 0 -2.167 0.066 -1.975
16 O1 O O1 N N N 0 -3.004 -0.728 -2.667
17 O2 O O2 N N N 0 -2.488 1.207 -1.72
18 HD1 H HD1 N N N 0 1.629 -1.499 2.691
19 HE1 H HE1 N N N 0 -0.061 -1.925 4.429
20 HZ H HZ N N N 0 -1.974 -0.396 4.688
21 HE2 H HE2 N N N 0 -2.194 1.56 3.209
22 HD2 H HD2 N N N 0 -0.5 1.989 1.475
23 HB3 H 1HB N N N 0 2.668 0.149 1.242
24 HB2 H 2HB N N N 0 1.777 1.603 0.733
25 HA H HA N N N 0 1.216 -1.246 -0.205
26 HXT H HXT N N Y 0 2.871 1.32 -2.936
27 H H HN N N N 0 -0.262 1.252 -0.624
28 HO1 H HO1 N N N 0 -3.86 -0.389 -2.961



NDF : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CD1 CE1 C C doub 1.38 N Y
2 CD1 CG C C sing 1.38 N Y
3 CD1 HD1 C H sing 1.08 N N
4 CE1 CZ C C sing 1.38 N Y
5 CE1 HE1 C H sing 1.08 N N
6 CZ CE2 C C doub 1.38 N Y
7 CZ HZ C H sing 1.08 N N
8 CE2 CD2 C C sing 1.38 N Y
9 CE2 HE2 C H sing 1.08 N N
10 CD2 CG C C doub 1.38 N Y
11 CD2 HD2 C H sing 1.08 N N
12 CG CB C C sing 1.51 N N
13 CB CA C C sing 1.53 N N
14 CB HB3 C H sing 1.09 N N
15 CB HB2 C H sing 1.09 N N
16 CA C C C sing 1.51 N N
17 CA N C N sing 1.46 N N
18 CA HA C H sing 1.09 N N
19 C O C O doub 1.21 N N
20 C OXT C O sing 1.34 N N
21 OXT HXT O H sing 0.97 N N
22 N C2 N C sing 1.35 N N
23 N H N H sing 0.97 N N
24 C2 O2' C O doub 1.21 N N
25 C2 C1 C C sing 1.49 N N
26 C1 O1 C O sing 1.35 N N
27 C1 O2 C O doub 1.21 N N
28 O1 HO1 O H sing 0.97 N N



NDF : Used in PDB Entries

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