Chemical Components in the PDB

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9VL : Summary

Code

9VL

One-letter code

X

Molecule name

(2S)-2-azanyl-6-[(2-bromophenyl)methoxycarbonylamino]hexanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{S})-2-azanyl-6-[(2-bromophenyl)methoxycarbonylamino]hexanoic acid

Formula

C14 H19 Br N2 O4

Formal charge

0

Molecular weight

359.216 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N[CH](CCCCNC(=O)OCc1ccccc1Br)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 c1ccc(c(c1)COC(=O)NCCCCC(C(=O)O)N)Br
Canonical SMILES CACTVS 3.385 N[C@@H](CCCCNC(=O)OCc1ccccc1Br)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc(c(c1)COC(=O)NCCCC[C@@H](C(=O)O)N)Br

IUPAC InChI

InChI=1S/C14H19BrN2O4/c15-11-6-2-1-5-10(11)9-21-14(20)17-8-4-3-7-12(16)13(18)19/h1-2,5-6,12H,3-4,7-9,16H2,(H,17,20)(H,18,19)/t12-/m0/s1

IUPAC InChI key

YGZWYMNBUCDJRQ-LBPRGKRZSA-N
9VL

wwPDB Information

Atom count

40 (21 without Hydrogen)

Polymer type

Amino Acid

Type description

peptide linking

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2018-08-16

Last modified at

2019-04-12

Status

Released

Obsoleted

Not Assigned



9VL : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C15 C C1 N Y N 0 3.678 -0.836 0.051
2 C20 C C2 N Y N 0 4.39 -3.116 0.217
3 C21 C C3 N Y N 0 3.374 -2.181 0.147
4 C C C4 N N N 0 -8.457 -0.332 -0.177
5 CA C C5 S N N 0 -7.232 0.543 -0.106
6 CB C C6 N N N 0 -5.981 -0.335 -0.038
7 CG C C7 N N N 0 -4.734 0.549 -0.092
8 CD C C8 N N N 0 -3.483 -0.33 -0.025
9 CE C C9 N N N 0 -2.235 0.554 -0.079
10 C11 C C10 N N N 0 0.185 0.279 -0.046
11 C14 C C11 N N N 0 2.57 0.183 -0.026
12 C16 C C12 N Y N 0 4.998 -0.425 0.03
13 C18 C C13 N Y N 0 6.015 -1.361 0.1
14 C19 C C14 N Y N 0 5.71 -2.706 0.191
15 N N N1 N N N 0 -7.303 1.388 1.094
16 NZ N N2 N N N 0 -1.038 -0.287 -0.014
17 O O O1 N N N 0 -9.111 -0.538 0.818
18 OXT O O2 N N Y 0 -8.822 -0.883 -1.345
19 O12 O O3 N N N 0 0.294 1.486 -0.128
20 O13 O O4 N N N 0 1.286 -0.494 0.014
21 BR BR BR1 N N N 0 5.414 1.415 -0.095
22 H20 H H1 N N N 0 4.153 -4.167 0.293
23 H21 H H2 N N N 0 2.343 -2.502 0.168
24 HA H H3 N N N 0 -7.185 1.175 -0.993
25 HB2 H H4 N N N 0 -5.985 -0.902 0.893
26 HB3 H H5 N N N 0 -5.975 -1.024 -0.883
27 HG2 H H6 N N N 0 -4.73 1.115 -1.023
28 HG3 H H7 N N N 0 -4.74 1.237 0.752
29 HD2 H H8 N N N 0 -3.487 -0.896 0.906
30 HD3 H H9 N N N 0 -3.477 -1.019 -0.869
31 HE2 H H10 N N N 0 -2.232 1.121 -1.01
32 HE3 H H11 N N N 0 -2.242 1.243 0.766
33 H12 H H12 N N N 0 2.646 0.866 0.82
34 H13 H H13 N N N 0 2.656 0.744 -0.956
35 H18 H H14 N N N 0 7.046 -1.04 0.083
36 H19 H H15 N N N 0 6.504 -3.437 0.245
37 H H H16 N N N 0 -7.347 0.825 1.93
38 H2 H H17 N N Y 0 -6.525 2.029 1.13
39 HXT H H20 N N Y 0 -9.615 -1.436 -1.341
40 HZ H H19 N N N 0 -1.125 -1.251 0.052



9VL : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 C21 C C doub 1.38 N Y
2 C20 C19 C C sing 1.38 N Y
3 C21 C15 C C sing 1.38 N Y
4 C19 C18 C C doub 1.38 N Y
5 C15 C14 C C sing 1.51 N N
6 C15 C16 C C doub 1.38 N Y
7 C18 C16 C C sing 1.38 N Y
8 C14 O13 C O sing 1.45 N N
9 C16 BR C BR sing 1.89 N N
10 O13 C11 O C sing 1.35 N N
11 O12 C11 O C doub 1.21 N N
12 C11 NZ C N sing 1.35 N N
13 CE NZ C N sing 1.46 N N
14 CE CD C C sing 1.53 N N
15 CD CG C C sing 1.53 N N
16 CG CB C C sing 1.53 N N
17 CB CA C C sing 1.53 N N
18 O C O C doub 1.21 N N
19 CA C C C sing 1.51 N N
20 CA N C N sing 1.47 N N
21 C OXT C O sing 1.34 N N
22 C20 H20 C H sing 1.08 N N
23 C21 H21 C H sing 1.08 N N
24 CA HA C H sing 1.09 N N
25 CB HB2 C H sing 1.09 N N
26 CB HB3 C H sing 1.09 N N
27 CG HG2 C H sing 1.09 N N
28 CG HG3 C H sing 1.09 N N
29 CD HD2 C H sing 1.09 N N
30 CD HD3 C H sing 1.09 N N
31 CE HE2 C H sing 1.09 N N
32 CE HE3 C H sing 1.09 N N
33 C14 H12 C H sing 1.09 N N
34 C14 H13 C H sing 1.09 N N
35 C18 H18 C H sing 1.08 N N
36 C19 H19 C H sing 1.08 N N
37 N H N H sing 1.01 N N
38 N H2 N H sing 1.01 N N
39 NZ HZ N H sing 0.97 N N
40 OXT HXT O H sing 0.97 N N



9VL : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9VL 6abl Open in New Window Bound ligand 1 1