Chemical Components in the PDB

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YXZ : Summary

Code

YXZ

One-letter code

X

Molecule name

chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium

Systematic names

ProgramVersionName
ACDLabs 12.01 chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium

Formula

C15 H20 Cl N4 Ru

Formal charge

0

Molecular weight

392.869 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Cl[Ru]3n1ccccc1N(c2n3cccc2)CCCCCN
SMILES CACTVS 3.370 NCCCCCN1c2ccccn2|[Ru](Cl)|n3ccccc13
SMILES OpenEye OEToolkits 1.7.6 C1=CC=[N]2C(=C1)N(C3=[N]([Ru]2Cl)C=CC=C3)CCCCCN
Canonical SMILES CACTVS 3.370 NCCCCCN1c2ccccn2|[Ru](Cl)|n3ccccc13
Canonical SMILES OpenEye OEToolkits 1.7.6 C1=CC=[N]2C(=C1)N(C3=[N]([Ru]2Cl)C=CC=C3)CCCCCN

IUPAC InChI

InChI=1S/C15H20N4.ClH.Ru/c16-10-4-1-7-13-19(14-8-2-5-11-17-14)15-9-3-6-12-18-15;;/h2-3,5-6,8-9,11-12H,1,4,7,10,13,16H2;1H;/q;;+1/p-1

IUPAC InChI key

IIQHAXSUPAXJMA-UHFFFAOYSA-M
YXZ

wwPDB Information

Atom count

41 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-24

Last modified at

2014-06-20

Status

Released

Obsoleted

Not Assigned



YXZ : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CL CL CL N N N 0
2 CAL C CAL N Y N 0
3 CAH C CAH N Y N 0
4 CAF C CAF N Y N 0
5 CAJ C CAJ N Y N 0
6 NAU N NAU N Y N 0
7 CBA C CBA N Y N 0
8 NBF N NBF N N N 0
9 CBB C CBB N Y N 0
10 CAM C CAM N Y N 0
11 CAI C CAI N Y N 0
12 CAG C CAG N Y N 0
13 CAK C CAK N Y N 0
14 NAV N NAV N Y N 0
15 CAR C CAR N N N 0
16 CAP C CAP N N N 0
17 CAN C CAN N N N 0
18 CAO C CAO N N N 0
19 CAQ C CAQ N N N 0
20 NBE N NBE N N N 0
21 RU RU RU N N N 0
22 H1 H H1 N N N 0
23 H2 H H2 N N N 0
24 H3 H H3 N N N 0
25 H4 H H4 N N N 0
26 H5 H H5 N N N 0
27 H6 H H6 N N N 0
28 H7 H H7 N N N 0
29 H8 H H8 N N N 0
30 H9 H H9 N N N 0
31 H10 H H10 N N N 0
32 H11 H H11 N N N 0
33 H12 H H12 N N N 0
34 H13 H H13 N N N 0
35 H14 H H14 N N N 0
36 H15 H H15 N N N 0
37 H16 H H16 N N N 0
38 H17 H H17 N N N 0
39 H18 H H18 N N N 0
40 H20 H H20 N N N 0
41 H21 H H21 N N N 0



YXZ : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAF CAH C C doub N Y
2 CAF CAJ C C sing N Y
3 CAH CAL C C sing N Y
4 CAJ NAU C N doub N Y
5 CAL CBA C C doub N Y
6 NAU CBA N C sing N Y
7 NAU RU N RU sing N N
8 CBA NBF C N sing N N
9 RU NAV RU N sing N N
10 RU CL RU CL sing N N
11 NBF CBB N C sing N N
12 NBF CAR N C sing N N
13 CBB NAV C N doub N Y
14 CBB CAM C C sing N Y
15 NAV CAK N C sing N Y
16 CAP CAR C C sing N N
17 CAP CAN C C sing N N
18 CAM CAI C C doub N Y
19 CAK CAG C C doub N Y
20 CAO CAN C C sing N N
21 CAO CAQ C C sing N N
22 CAI CAG C C sing N Y
23 CAQ NBE C N sing N N
24 CAL H1 C H sing N N
25 CAH H2 C H sing N N
26 CAF H3 C H sing N N
27 CAJ H4 C H sing N N
28 CAM H5 C H sing N N
29 CAI H6 C H sing N N
30 CAG H7 C H sing N N
31 CAK H8 C H sing N N
32 CAR H9 C H sing N N
33 CAP H10 C H sing N N
34 CAN H11 C H sing N N
35 CAN H12 C H sing N N
36 CAO H13 C H sing N N
37 CAO H14 C H sing N N
38 CAQ H15 C H sing N N
39 CAQ H16 C H sing N N
40 NBE H17 N H sing N N
41 NBE H18 N H sing N N
42 CAR H20 C H sing N N
43 CAP H21 C H sing N N



YXZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YXZ 6h8t Open in New Window Bound ligand 1 1