Chemical Components in the PDB

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3V6 : Summary

Code

3V6

One-letter code

X

Molecule name

Bactobolin A

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(3S,4R,4aR,5S,6R)-3-(dichloromethyl)-5,8-dihydroxy-3,6-dimethyl-1-oxo-3,4,4a,5,6,7-hexahydro-1H-isochromen-4-yl]-L-alaninamide
OpenEye OEToolkits 1.9.2 (2S)-N-[(3S,4R,4aR,5S,6R)-3-[bis(chloranyl)methyl]-3,6-dimethyl-5,8-bis(oxidanyl)-1-oxidanylidene-4a,5,6,7-tetrahydro-4H-isochromen-4-yl]-2-azanyl-propanamide

Formula

C15 H22 Cl2 N2 O5

Formal charge

0

Molecular weight

381.252 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 ClC(Cl)C2(OC(=O)C1=C(O)CC(C(O)C1C2NC(=O)C(N)C)C)C
SMILES CACTVS 3.385 C[CH](N)C(=O)N[CH]1[CH]2[CH](O)[CH](C)CC(=C2C(=O)O[C]1(C)C(Cl)Cl)O
SMILES OpenEye OEToolkits 1.9.2 CC1CC(=C2C(C1O)C(C(OC2=O)(C)C(Cl)Cl)NC(=O)C(C)N)O
Canonical SMILES CACTVS 3.385 C[C@H](N)C(=O)N[C@@H]1[C@@H]2[C@@H](O)[C@H](C)CC(=C2C(=O)O[C@]1(C)C(Cl)Cl)O
Canonical SMILES OpenEye OEToolkits 1.9.2 C[C@@H]1CC(=C2[C@@H]([C@H]1O)[C@H]([C@@](OC2=O)(C)C(Cl)Cl)NC(=O)[C@H](C)N)O

IUPAC InChI

InChI=1S/C15H22Cl2N2O5/c1-5-4-7(20)8-9(10(5)21)11(19-12(22)6(2)18)15(3,14(16)17)24-13(8)23/h5-6,9-11,14,20-21H,4,18H2,1-3H3,(H,19,22)/t5-,6+,9+,10+,11-,15+/m1/s1

IUPAC InChI key

RREHSYIRMHYJHY-RQGKCFPDSA-N
3V6

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

2014-11-11

Last modified at

2015-01-16

Status

Released

Obsoleted

Not Assigned



3V6 : 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 CLI CL CL1 N N N 0 -3.624 -1.504 -0.459
2 CAT C C1 N N N 0 -2.223 -0.381 -0.299
3 CLJ CL CL2 N N N 0 -2.825 1.31 -0.124
4 CAX C C2 S N N 0 -1.403 -0.761 0.936
5 CAC C C3 N N N 0 -2.254 -0.514 2.184
6 OAM O O1 N N N 0 -1.086 -2.144 0.865
7 CAO C C4 N N N 0 -0.144 -2.513 -0.041
8 OAE O O2 N N N 0 -0.322 -3.414 -0.839
9 CAQ C C5 N N N 0 1.073 -1.764 0.012
10 CAN C C6 N N N 0 2.078 -2.064 -0.805
11 OAG O O3 N N N 0 1.909 -3.08 -1.675
12 CAK C C7 N N N 0 3.39 -1.335 -0.812
13 CAS C C8 R N N 0 3.559 -0.558 0.496
14 CAB C C9 N N N 0 4.777 0.362 0.394
15 CAU C C10 S N N 0 2.297 0.28 0.728
16 OAH O O4 N N N 0 2.506 1.163 1.832
17 CAW C C11 R N N 0 1.128 -0.659 1.036
18 CAV C C12 R N N 0 -0.175 0.131 0.999
19 NAL N N1 N N N 0 -0.164 1.005 -0.177
20 C C C13 N N N 0 -0.089 2.342 -0.022
21 O O O5 N N N 0 0.06 2.816 1.085
22 CA C C14 S N N 0 -0.19 3.246 -1.222
23 CB C C15 N N N 0 0.941 2.923 -2.201
24 N N N2 N N N 0 -0.079 4.646 -0.791
25 H1 H H1 N N N 0 -1.596 -0.453 -1.188
26 H2 H H2 N N N 0 -3.155 -1.125 2.135
27 H3 H H3 N N N 0 -1.681 -0.781 3.072
28 H4 H H4 N N N 0 -2.531 0.539 2.233
29 H5 H H5 N N N 0 2.651 -3.283 -2.262
30 H6 H H6 N N N 0 4.203 -2.053 -0.915
31 H7 H H7 N N N 0 3.414 -0.64 -1.652
32 H8 H H8 N N N 0 3.695 -1.257 1.321
33 H9 H H9 N N N 0 4.634 1.064 -0.427
34 H10 H H10 N N N 0 4.894 0.914 1.327
35 H11 H H11 N N N 0 5.669 -0.235 0.21
36 H12 H H12 N N N 0 2.075 0.861 -0.167
37 H13 H H13 N N N 0 3.239 1.781 1.709
38 H14 H H14 N N N 0 1.261 -1.09 2.028
39 H15 H H15 N N N 0 -0.235 0.749 1.894
40 H16 H H16 N N N 0 -0.212 0.622 -1.066
41 H17 H H17 N N N 0 -1.151 3.092 -1.714
42 H18 H H18 N N N 0 0.859 1.885 -2.521
43 H19 H H19 N N N 0 0.868 3.578 -3.069
44 H20 H H20 N N N 0 1.902 3.077 -1.71
45 H21 H H21 N N N 0 0.775 4.8 -0.276
46 H22 H H22 N N N 0 -0.144 5.273 -1.579



3V6 : Chemical Bonds

Total Number of Bonds: 47
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CLJ CAT CL C sing 1.8 N N
2 CAT CLI C CL sing 1.8 N N
3 CAT CAX C C sing 1.53 N N
4 CB CA C C sing 1.53 N N
5 CA N C N sing 1.47 N N
6 CA C C C sing 1.51 N N
7 OAM CAX O C sing 1.42 N N
8 OAM CAO O C sing 1.36 N N
9 OAE CAO O C doub 1.22 N N
10 CAX CAC C C sing 1.53 N N
11 CAX CAV C C sing 1.52 N N
12 C NAL C N sing 1.35 N N
13 C O C O doub 1.21 N N
14 CAO CAQ C C sing 1.43 N N
15 NAL CAV N C sing 1.47 N N
16 CAV CAW C C sing 1.52 N N
17 OAG CAN O C sing 1.35 N N
18 CAQ CAW C C sing 1.51 N N
19 CAQ CAN C C doub 1.33 N N
20 CAW CAU C C sing 1.53 N N
21 CAN CAK C C sing 1.5 N N
22 CAU OAH C O sing 1.43 N N
23 CAU CAS C C sing 1.53 N N
24 CAK CAS C C sing 1.53 N N
25 CAS CAB C C sing 1.53 N N
26 CAT H1 C H sing 1.09 N N
27 CAC H2 C H sing 1.09 N N
28 CAC H3 C H sing 1.09 N N
29 CAC H4 C H sing 1.09 N N
30 OAG H5 O H sing 0.97 N N
31 CAK H6 C H sing 1.09 N N
32 CAK H7 C H sing 1.09 N N
33 CAS H8 C H sing 1.09 N N
34 CAB H9 C H sing 1.09 N N
35 CAB H10 C H sing 1.09 N N
36 CAB H11 C H sing 1.09 N N
37 CAU H12 C H sing 1.09 N N
38 OAH H13 O H sing 0.97 N N
39 CAW H14 C H sing 1.09 N N
40 CAV H15 C H sing 1.09 N N
41 NAL H16 N H sing 0.97 N N
42 CA H17 C H sing 1.09 N N
43 CB H18 C H sing 1.09 N N
44 CB H19 C H sing 1.09 N N
45 CB H20 C H sing 1.09 N N
46 N H21 N H sing 1.01 N N
47 N H22 N H sing 1.01 N N



3V6 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
3V6 4wt8 Open in New Window Bound ligand 2 1