Chemical Components in the PDB

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V20 : Summary

Code

V20

One-letter code

X

Molecule name

N6^-[(1R)-2-[(1S)-1-CARBOXY-2-(METHYLSULFANYL)ETHOXY]-2-OXO-1-(SULFANYLMETHYL)ETHYL]-6-OXO-L-LYSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 N~6~-[(1R)-2-[(1S)-1-carboxy-2-(methylsulfanyl)ethoxy]-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine
OpenEye OEToolkits 1.5.0 (2S)-2-amino-6-[[(2R)-1-[(2S)-1-hydroxy-3-methylsulfanyl-1-oxo-propan-2-yl]oxy-1-oxo-3-sulfanyl-propan-2-yl]amino]-6-oxo-hexanoic acid

Formula

C13 H22 N2 O7 S2

Formal charge

0

Molecular weight

382.453 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(OC(=O)C(NC(=O)CCCC(C(=O)O)N)CS)CSC
SMILES CACTVS 3.341 CSC[CH](OC(=O)[CH](CS)NC(=O)CCC[CH](N)C(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CSCC(C(=O)O)OC(=O)C(CS)NC(=O)CCCC(C(=O)O)N
Canonical SMILES CACTVS 3.341 CSC[C@@H](OC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CSC[C@H](C(=O)O)OC(=O)[C@H](CS)NC(=O)CCC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C13H22N2O7S2/c1-24-6-9(12(19)20)22-13(21)8(5-23)15-10(16)4-2-3-7(14)11(17)18/h7-9,23H,2-6,14H2,1H3,(H,15,16)(H,17,18)(H,19,20)/t7-,8-,9+/m0/s1

IUPAC InChI key

ZBJXRZZOCYDPEK-XHNCKOQMSA-N
V20

wwPDB Information

Atom count

46 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-09-04

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



V20 : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O O O N N N 0 7.98 2.009 0.399
2 C C C N N N 0 7.686 0.7 0.401
3 OXT O OXT N N N 0 8.4 -0.079 0.988
4 CA C CA S N N 0 6.465 0.2 -0.328
5 N N N N N N 0 6.607 -1.238 -0.591
6 CB C CB N N N 0 5.223 0.442 0.532
7 CAJ C CAJ N N N 0 3.972 0.05 -0.257
8 CAL C CAL N N N 0 2.73 0.292 0.603
9 CAT C CAT N N N 0 1.498 -0.094 -0.175
10 OAE O OAE N N N 0 1.603 -0.52 -1.305
11 NAO N NAO N N N 0 0.28 0.035 0.386
12 CAW C CAW R N N 0 -0.918 -0.34 -0.37
13 CAK C CAK N N N 0 -1.168 -1.842 -0.217
14 SAI S SAI N N N 0 0.261 -2.76 -0.853
15 CAU C CAU N N N 0 -2.105 0.423 0.159
16 OAF O OAF N N N 0 -1.965 1.201 1.073
17 OAP O OAP N N N 0 -3.318 0.239 -0.386
18 CAX C CAX S N N 0 -4.415 1.008 0.174
19 CAS C CAS N N N 0 -4.537 2.318 -0.561
20 OAD O OAD N N N 0 -5.422 3.239 -0.149
21 OAH O OAH N N N 0 -3.837 2.54 -1.52
22 CAN C CAN N N N 0 -5.718 0.219 0.027
23 SAQ S SAQ N N N 0 -5.627 -1.289 1.031
24 CAA C CAA N N N 0 -7.234 -2.076 0.731
25 H H H N N N 0 8.774 2.282 0.88
26 HA H HA N N N 0 6.363 0.734 -1.273
27 HN1 H 1HN N N N 0 6.703 -1.755 0.27
28 HN2 H 2HN N N N 0 5.831 -1.584 -1.135
29 HBC1 H 1HBC N N N 0 5.285 -0.161 1.438
30 HBC2 H 2HBC N N N 0 5.168 1.497 0.801
31 HAJ1 H 1HAJ N N N 0 3.911 0.654 -1.163
32 HAJ2 H 2HAJ N N N 0 4.028 -1.005 -0.526
33 HAL1 H 1HAL N N N 0 2.792 -0.311 1.508
34 HAL2 H 2HAL N N N 0 2.674 1.347 0.872
35 HAO H HAO N N N 0 0.196 0.376 1.29
36 HAW H HAW N N N 0 -0.772 -0.101 -1.423
37 HAK1 H 1HAK N N N 0 -1.314 -2.08 0.837
38 HAK2 H 2HAK N N N 0 -2.059 -2.121 -0.779
39 HAI H HAI N N N 0 -0.093 -4.043 -0.658
40 HAX H HAX N N N 0 -4.224 1.199 1.23
41 HAN1 H 1HAN N N N 0 -6.554 0.831 0.366
42 HAN2 H 2HAN N N N 0 -5.864 -0.05 -1.019
43 HAD H HAD N N N 0 -5.464 4.064 -0.651
44 HAA1 H 1HAA N N N 0 -7.293 -3.008 1.294
45 HAA2 H 2HAA N N N 0 -8.032 -1.407 1.052
46 HAA3 H 3HAA N N N 0 -7.343 -2.287 -0.333



V20 : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O C O C sing 1.34 N N
2 C OXT C O doub 1.21 N N
3 C CA C C sing 1.51 N N
4 CA N C N sing 1.47 N N
5 CA CB C C sing 1.53 N N
6 CB CAJ C C sing 1.53 N N
7 CAJ CAL C C sing 1.53 N N
8 CAL CAT C C sing 1.51 N N
9 CAT OAE C O doub 1.21 N N
10 CAT NAO C N sing 1.35 N N
11 NAO CAW N C sing 1.47 N N
12 CAW CAK C C sing 1.53 N N
13 CAW CAU C C sing 1.51 N N
14 CAK SAI C S sing 1.81 N N
15 CAU OAF C O doub 1.21 N N
16 CAU OAP C O sing 1.34 N N
17 OAP CAX O C sing 1.45 N N
18 CAX CAS C C sing 1.51 N N
19 CAX CAN C C sing 1.53 N N
20 CAS OAD C O sing 1.34 N N
21 CAS OAH C O doub 1.21 N N
22 CAN SAQ C S sing 1.81 N N
23 SAQ CAA S C sing 1.81 N N
24 O H O H sing 0.97 N N
25 CA HA C H sing 1.09 N N
26 N HN1 N H sing 1.01 N N
27 N HN2 N H sing 1.01 N N
28 CB HBC1 C H sing 1.09 N N
29 CB HBC2 C H sing 1.09 N N
30 CAJ HAJ1 C H sing 1.09 N N
31 CAJ HAJ2 C H sing 1.09 N N
32 CAL HAL1 C H sing 1.09 N N
33 CAL HAL2 C H sing 1.09 N N
34 NAO HAO N H sing 0.97 N N
35 CAW HAW C H sing 1.09 N N
36 CAK HAK1 C H sing 1.09 N N
37 CAK HAK2 C H sing 1.09 N N
38 SAI HAI S H sing 1.35 N N
39 CAX HAX C H sing 1.09 N N
40 CAN HAN1 C H sing 1.09 N N
41 CAN HAN2 C H sing 1.09 N N
42 OAD HAD O H sing 0.97 N N
43 CAA HAA1 C H sing 1.09 N N
44 CAA HAA2 C H sing 1.09 N N
45 CAA HAA3 C H sing 1.09 N N



V20 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
V20 2vau Open in New Window Bound ligand 1 1