Chemical Components in the PDB

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J0J : Summary

Code

J0J

One-letter code

X

Molecule name

D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine

Systematic names

ProgramVersionName
ACDLabs 12.01 D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine
OpenEye OEToolkits 1.7.6 (2R,6S)-2-azanyl-6-[[(4R)-4-[[(2R)-2-azanylpropanoyl]amino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-7-oxidanylidene-7-[[(2R)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]heptanoic acid

Formula

C18 H31 N5 O9

Formal charge

0

Molecular weight

461.467 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC(C(=O)O)CCC(=O)NC(C(=O)NC(C(=O)O)C)CCCC(C(=O)O)N)C(N)C
SMILES CACTVS 3.370 C[CH](N)C(=O)N[CH](CCC(=O)N[CH](CCC[CH](N)C(O)=O)C(=O)N[CH](C)C(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(C(=O)NC(CCC(=O)NC(CCCC(C(=O)O)N)C(=O)NC(C)C(=O)O)C(=O)O)N
Canonical SMILES CACTVS 3.370 C[C@@H](N)C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@@H](N)C(O)=O)C(=O)N[C@H](C)C(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O)O)N)C(=O)N[C@H](C)C(=O)O)C(=O)O)N

IUPAC InChI

InChI=1S/C18H31N5O9/c1-8(19)14(25)23-12(18(31)32)6-7-13(24)22-11(5-3-4-10(20)17(29)30)15(26)21-9(2)16(27)28/h8-12H,3-7,19-20H2,1-2H3,(H,21,26)(H,22,24)(H,23,25)(H,27,28)(H,29,30)(H,31,32)/t8-,9-,10-,11+,12-/m1/s1

IUPAC InChI key

VFGFFQOPKZHQLZ-PZWNZHSQSA-N

Has sub-components

DAL , DGL , API , DAL
J0J

wwPDB Information

Atom count

63 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-21

Last modified at

2013-07-12

Status

Released

Obsoleted

Not Assigned



J0J : Atoms of Molecule

Total Number of Atoms: 63
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N03 N N03 N N N 0 -6.702 2.216 1.72
2 C02 C C02 R N N 0 -6.04 1.788 0.48
3 C01 C C01 N N N 0 -7.024 1.895 -0.687
4 C04 C C04 N N N 0 -5.581 0.36 0.622
5 O05 O O05 N N N 0 -6.077 -0.355 1.466
6 N06 N N06 N N N 0 -4.62 -0.123 -0.19
7 C07 C C07 R N N 0 -4.174 -1.512 -0.052
8 C30 C C30 N N N 0 -5.089 -2.414 -0.839
9 O31 O O31 N N N 0 -6.018 -1.944 -1.452
10 C08 C C08 N N N 0 -2.746 -1.644 -0.585
11 C09 C C09 N N N 0 -1.796 -0.825 0.292
12 C10 C C10 N N N 0 -0.389 -0.956 -0.232
13 O11 O O11 N N N 0 -0.168 -1.636 -1.211
14 O32 O O32 N N N 0 -4.872 -3.738 -0.859
15 C22 C C22 N N N 0 2.624 -1.687 0.441
16 C13 C C13 S N N 0 1.99 -0.442 -0.124
17 C14 C C14 N N N 0 2.807 0.781 0.297
18 C15 C C15 N N N 0 2.237 2.031 -0.378
19 C16 C C16 N N N 0 3.054 3.255 0.042
20 C17 C C17 R N N 0 2.484 4.504 -0.633
21 C19 C C19 N N N 0 3.361 5.689 -0.317
22 O23 O O23 N N N 0 1.995 -2.399 1.196
23 O20 O O20 N N N 0 3.037 6.466 0.549
24 O21 O O21 N N N 0 4.501 5.881 -0.999
25 N12 N N12 N N N 0 0.623 -0.315 0.386
26 N18 N N18 N N N 0 1.125 4.754 -0.134
27 N24 N N24 N N N 0 3.889 -2.01 0.108
28 C25 C C25 R N N 0 4.505 -3.221 0.658
29 C26 C C26 N N N 0 5.102 -2.911 2.032
30 C27 C C27 N N N 0 5.596 -3.694 -0.268
31 O28 O O28 N N N 0 5.834 -3.083 -1.283
32 O29 O O29 N N N 0 6.302 -4.794 0.035
33 HN03 H HN03 N N N 0 -7.504 1.637 1.919
34 HN0A H HN0A N N N 0 -6.054 2.216 2.494
35 H02 H H02 N N N 0 -5.179 2.429 0.288
36 H01 H H01 N N N 0 -7.885 1.254 -0.495
37 H07 H H07 N N N 0 -4.197 -1.798 0.999
38 H01A H H01A N N N 0 -7.356 2.928 -0.789
39 H01B H H01B N N N 0 -6.533 1.578 -1.607
40 HN06 H HN06 N N N 0 -4.223 0.449 -0.865
41 H08 H H08 N N N 0 -2.446 -2.692 -0.564
42 H08A H H08A N N N 0 -2.704 -1.274 -1.609
43 H09 H H09 N N N 0 -2.096 0.223 0.272
44 H09A H H09A N N N 0 -1.837 -1.195 1.317
45 HO32 H HO32 N N N 0 -5.485 -4.276 -1.378
46 H13 H H13 N N N 0 1.967 -0.508 -1.212
47 H14 H H14 N N N 0 2.756 0.898 1.379
48 H14A H H14A N N N 0 3.845 0.646 -0.006
49 H15 H H15 N N N 0 2.288 1.914 -1.461
50 H15A H H15A N N N 0 1.199 2.166 -0.076
51 H16 H H16 N N N 0 3.003 3.371 1.125
52 H16A H H16A N N N 0 4.092 3.12 -0.26
53 H17 H H17 N N N 0 2.453 4.352 -1.712
54 HO21 H HO21 N N N 0 5.03 6.655 -0.762
55 HN12 H HN12 N N N 0 0.445 0.229 1.169
56 HN18 H HN18 N N N 0 0.503 4.002 -0.389
57 HN1A H HN1A N N N 0 1.128 4.898 0.865
58 HN24 H HN24 N N N 0 4.392 -1.441 -0.495
59 H25 H H25 N N N 0 3.749 -4.0 0.757
60 H26 H H26 N N N 0 5.56 -3.811 2.441
61 H26A H H26A N N N 0 5.857 -2.131 1.933
62 H26B H H26B N N N 0 4.312 -2.568 2.702
63 HO29 H HO29 N N N 0 6.992 -5.059 -0.59



J0J : Chemical Bonds

Total Number of Bonds: 62
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 H01B C01 H C sing 1.09 N N
2 C01 H01A C H sing 1.09 N N
3 C01 H01 C H sing 1.09 N N
4 C01 C02 C C sing 1.53 N N
5 C04 C02 C C sing 1.51 N N
6 C02 N03 C N sing 1.47 N N
7 C02 H02 C H sing 1.09 N N
8 N03 HN03 N H sing 1.01 N N
9 N03 HN0A N H sing 1.01 N N
10 N06 C04 N C sing 1.35 N N
11 C04 O05 C O doub 1.21 N N
12 C07 N06 C N sing 1.47 N N
13 HN06 N06 H N sing 0.97 N N
14 C08 C07 C C sing 1.53 N N
15 C30 C07 C C sing 1.51 N N
16 C07 H07 C H sing 1.09 N N
17 H08 C08 H C sing 1.09 N N
18 C09 C08 C C sing 1.53 N N
19 C08 H08A C H sing 1.09 N N
20 C10 C09 C C sing 1.51 N N
21 H09 C09 H C sing 1.09 N N
22 C09 H09A C H sing 1.09 N N
23 O11 C10 O C doub 1.21 N N
24 N12 C10 N C sing 1.35 N N
25 C13 N12 C N sing 1.46 N N
26 N12 HN12 N H sing 0.97 N N
27 C22 C13 C C sing 1.51 N N
28 H13 C13 H C sing 1.09 N N
29 C13 C14 C C sing 1.53 N N
30 H14 C14 H C sing 1.09 N N
31 C14 C15 C C sing 1.53 N N
32 C14 H14A C H sing 1.09 N N
33 H15 C15 H C sing 1.09 N N
34 C15 C16 C C sing 1.53 N N
35 C15 H15A C H sing 1.09 N N
36 H16 C16 H C sing 1.09 N N
37 C17 C16 C C sing 1.53 N N
38 C16 H16A C H sing 1.09 N N
39 C19 C17 C C sing 1.51 N N
40 C17 H17 C H sing 1.09 N N
41 C17 N18 C N sing 1.47 N N
42 HN18 N18 H N sing 1.01 N N
43 N18 HN1A N H sing 1.01 N N
44 O20 C19 O C doub 1.21 N N
45 O21 C19 O C sing 1.34 N N
46 O21 HO21 O H sing 0.97 N N
47 N24 C22 N C sing 1.35 N N
48 C22 O23 C O doub 1.21 N N
49 C25 N24 C N sing 1.47 N N
50 N24 HN24 N H sing 0.97 N N
51 C27 C25 C C sing 1.51 N N
52 C26 C25 C C sing 1.53 N N
53 C25 H25 C H sing 1.09 N N
54 H26B C26 H C sing 1.09 N N
55 H26 C26 H C sing 1.09 N N
56 C26 H26A C H sing 1.09 N N
57 O28 C27 O C doub 1.21 N N
58 C27 O29 C O sing 1.34 N N
59 O29 HO29 O H sing 0.97 N N
60 O31 C30 O C doub 1.21 N N
61 C30 O32 C O sing 1.34 N N
62 O32 HO32 O H sing 0.97 N N



J0J : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
J0J 4bol Open in New Window Bound ligand 2 1