Chemical Components in the PDB

pdbe.org/chem
spacer

PCX : Summary

Code

PCX

One-letter code

X

Molecule name

DEOXYGUANIDINOPROCLAVAMINIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-5-carbamimidamido-2-(2-oxoazetidin-1-yl)pentanoic acid
OpenEye OEToolkits 1.5.0 (2S)-5-carbamimidamido-2-(2-oxoazetidin-1-yl)pentanoic acid

Formula

C9 H16 N4 O3

Formal charge

0

Molecular weight

228.248 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N1C(=O)CC1)CCCNC(=[N@H])N
SMILES CACTVS 3.341 NC(=N)NCCC[CH](N1CCC1=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 [H]N=C(N)NCCCC(C(=O)O)N1CCC1=O
Canonical SMILES CACTVS 3.341 NC(=N)NCCC[C@H](N1CCC1=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 [H]/N=C(/N)\NCCC[C@@H](C(=O)O)N1CCC1=O

IUPAC InChI

InChI=1S/C9H16N4O3/c10-9(11)12-4-1-2-6(8(15)16)13-5-3-7(13)14/h6H,1-5H2,(H,15,16)(H4,10,11,12)/t6-/m0/s1

IUPAC InChI key

UYADDEKIZFRINK-LURJTMIESA-N
PCX

wwPDB Information

Atom count

32 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-02-12

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PCX : Atoms of Molecule

Total Number of Atoms: 32
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 -0.439 1.089 -0.961
2 C1 C C1 S N N 0 0.0090 2.277 -1.687
3 C2 C C2 N N N 0 1.475 2.15 -2.127
4 C4 C C4 N N N 0 1.745 1.017 -3.13
5 C5 C C5 N N N 0 3.205 0.971 -3.579
6 N2 N N2 N N N 0 3.423 -0.1 -4.522
7 C6 C C6 N N N 0 4.614 -0.442 -5.129
8 N3 N N3 N N N 0 5.716 0.31 -4.807
9 N4 N N4 N N N 0 4.683 -1.438 -5.972
10 C3 C C3 N N N 0 -0.923 2.488 -2.868
11 O1 O O1 N N N 0 -1.461 1.6 -3.516
12 O2 O O2 N N Y 0 -1.105 3.807 -3.14
13 C8 C C8 N N N 0 -0.012 0.518 0.169
14 C9 C C9 N N N 0 -1.089 -0.571 0.023
15 O4 O O4 N N N 0 0.865 0.777 0.96
16 C7 C C7 N N N 0 -1.494 0.171 -1.266
17 H1 H H1 N N N 0 -0.1 3.136 -1.014
18 H2C1 H 1H2C N N N 0 2.101 2.0 -1.239
19 H2C2 H 2H2C N N N 0 1.796 3.102 -2.571
20 H4C1 H 1H4C N N N 0 1.121 1.159 -4.02
21 H4C2 H 2H4C N N N 0 1.466 0.052 -2.691
22 H5C1 H 1H5C N N N 0 3.469 1.919 -4.059
23 H5C2 H 2H5C N N N 0 3.868 0.843 -2.717
24 H2 H H2 N N N 0 2.603 -0.654 -4.757
25 H3N1 H 1H3N N N N 0 5.673 1.084 -4.154
26 H3N2 H 2H3N N N N 0 6.622 0.111 -5.218
27 HA H HA N N N 0 -1.701 4.0 -3.895
28 H9C1 H 1H9C N N N 0 -0.687 -1.576 -0.122
29 H9C2 H 2H9C N N N 0 -1.834 -0.566 0.821
30 H7C1 H 1H7C N N N 0 -1.338 -0.384 -2.194
31 H7C2 H 2H7C N N N 0 -2.489 0.624 -1.251
32 HN1 H HN1 N N N 0 3.75 -1.854 -6.062



PCX : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C1 N C sing 1.46 N N
2 N1 C8 N C sing 1.34 N N
3 N1 C7 N C sing 1.43 N N
4 C1 C2 C C sing 1.54 N N
5 C1 C3 C C sing 1.52 N N
6 C1 H1 C H sing 1.1 N N
7 C2 C4 C C sing 1.54 N N
8 C2 H2C1 C H sing 1.1 N N
9 C2 H2C2 C H sing 1.1 N N
10 C4 C5 C C sing 1.53 N N
11 C4 H4C1 C H sing 1.1 N N
12 C4 H4C2 C H sing 1.1 N N
13 C5 N2 C N sing 1.44 N N
14 C5 H5C1 C H sing 1.09 N N
15 C5 H5C2 C H sing 1.09 N N
16 N2 C6 N C sing 1.38 N N
17 N2 H2 N H sing 1.02 N N
18 C6 N3 C N sing 1.37 N N
19 C6 N4 C N doub 1.31 N N
20 N3 H3N1 N H sing 1.01 N N
21 N3 H3N2 N H sing 1.01 N N
22 C3 O1 C O doub 1.22 N N
23 C3 O2 C O sing 1.36 N N
24 O2 HA O H sing 0.98 N N
25 C8 C9 C C sing 1.54 N N
26 C8 O4 C O doub 1.21 N N
27 C9 C7 C C sing 1.54 N N
28 C9 H9C1 C H sing 1.09 N N
29 C9 H9C2 C H sing 1.09 N N
30 C7 H7C1 C H sing 1.09 N N
31 C7 H7C2 C H sing 1.09 N N
32 HN1 N4 H N sing 1.03 N N



PCX : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
PCX 1gvg Open in New Window Bound ligand 1 1
PCX 1mc1 Open in New Window Bound ligand 2 1