Chemical Components in the PDB

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3KS : Summary

Code

3KS

One-letter code

X

Molecule name

N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine
OpenEye OEToolkits 1.9.2 (2S,6R)-2-[[(4R)-4-[[(2S)-2-acetamidopropanoyl]amino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-6-azanyl-heptanedioic acid

Formula

C17 H28 N4 O9

Formal charge

0

Molecular weight

432.426 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC(C(=O)O)CCCC(C(=O)O)N)CCC(C(=O)O)NC(=O)C(NC(=O)C)C
SMILES CACTVS 3.385 C[CH](NC(C)=O)C(=O)N[CH](CCC(=O)N[CH](CCC[CH](N)C(O)=O)C(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.9.2 CC(C(=O)NC(CCC(=O)NC(CCCC(C(=O)O)N)C(=O)O)C(=O)O)NC(=O)C
Canonical SMILES CACTVS 3.385 C[C@H](NC(C)=O)C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.9.2 C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O)O)N)C(=O)O)C(=O)O)NC(=O)C

IUPAC InChI

InChI=1S/C17H28N4O9/c1-8(19-9(2)22)14(24)21-12(17(29)30)6-7-13(23)20-11(16(27)28)5-3-4-10(18)15(25)26/h8,10-12H,3-7,18H2,1-2H3,(H,19,22)(H,20,23)(H,21,24)(H,25,26)(H,27,28)(H,29,30)/t8-,10+,11-,12+/m0/s1

IUPAC InChI key

TWGWYWBHDIWICS-ZDDJMSTPSA-N
3KS

wwPDB Information

Atom count

58 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-09-08

Last modified at

2014-12-19

Status

Released

Obsoleted

Not Assigned



3KS : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C15 C C1 N N N 0 -5.83 3.365 0.44
2 O8 O O1 N N N 0 -5.588 3.887 -0.628
3 C16 C C2 N N N 0 -6.886 3.95 1.342
4 N3 N N1 N N N 0 -5.158 2.259 0.817
5 C1 C C3 S N N 0 -4.132 1.691 -0.061
6 C2 C C5 N N N 0 -3.976 0.221 0.235
7 O7 O O2 N N N 0 -4.655 -0.3 1.094
8 C C C4 N N N 0 -2.801 2.404 0.183
9 N N N2 N N N 0 -3.081 -0.513 -0.455
10 C3 C C6 R N N 0 -2.93 -1.942 -0.168
11 C4 C C7 N N N 0 -3.956 -2.723 -0.948
12 O1 O O3 N N N 0 -4.734 -2.146 -1.669
13 C5 C C8 N N N 0 -1.526 -2.397 -0.573
14 C6 C C9 N N N 0 -0.489 -1.695 0.305
15 C7 C C10 N N N 0 0.893 -2.144 -0.094
16 O6 O O5 N N N 0 1.035 -2.946 -0.992
17 O O O4 N N N 0 -4.005 -4.06 -0.841
18 C9 C C12 N N N 0 3.654 -3.373 0.875
19 C8 C C11 S N N 0 3.316 -2.09 0.16
20 C10 C C13 N N N 0 4.332 -1.011 0.541
21 C11 C C14 N N N 0 4.065 0.253 -0.278
22 C12 C C15 N N N 0 5.081 1.332 0.103
23 C13 C C16 R N N 0 4.814 2.596 -0.716
24 C14 C C17 N N N 0 5.887 3.615 -0.432
25 O3 O O6 N N N 0 2.854 -3.872 1.63
26 O2 O O7 N N N 0 4.843 -3.961 0.672
27 O5 O O8 N N N 0 5.672 4.52 0.34
28 O4 O O9 N N N 0 7.082 3.518 -1.035
29 N1 N N3 N N N 0 1.973 -1.654 0.548
30 N2 N N4 N N N 0 3.503 3.15 -0.349
31 H161 H H3 N N N 0 -7.649 4.441 0.738
32 H162 H H2 N N N 0 -7.345 3.153 1.928
33 H163 H H1 N N N 0 -6.429 4.677 2.013
34 H31 H H4 N N N 0 -5.355 1.839 1.669
35 H11 H H5 N N N 0 -4.43 1.823 -1.101
36 HC1 H H6 N N N 0 -2.914 3.467 -0.031
37 HC2 H H7 N N N 0 -2.503 2.273 1.224
38 HC3 H H8 N N N 0 -2.037 1.982 -0.47
39 HN1 H H9 N N N 0 -2.538 -0.097 -1.142
40 H32 H H10 N N N 0 -3.074 -2.115 0.898
41 H51 H H12 N N N 0 -1.442 -3.476 -0.443
42 H52 H H13 N N N 0 -1.349 -2.143 -1.618
43 H61 H H15 N N N 0 -0.572 -0.617 0.175
44 H62 H H14 N N N 0 -0.666 -1.95 1.35
45 H1 H H11 N N N 0 -4.681 -4.517 -1.36
46 H81 H H17 N N N 0 3.348 -2.255 -0.917
47 H101 H H19 N N N 0 4.239 -0.783 1.602
48 H102 H H20 N N N 0 5.34 -1.372 0.334
49 H111 H H21 N N N 0 4.158 0.025 -1.34
50 H112 H H22 N N N 0 3.057 0.614 -0.071
51 H121 H H23 N N N 0 4.988 1.56 1.165
52 H122 H H24 N N N 0 6.089 0.971 -0.104
53 H131 H H25 N N N 0 4.819 2.349 -1.778
54 H2 H H18 N N N 0 5.014 -4.783 1.152
55 H4 H H29 N N N 0 7.739 4.195 -0.821
56 H12 H H16 N N N 0 1.86 -1.012 1.266
57 H21 H H27 N N N 0 3.473 3.387 0.632
58 H22 H H26 N N N 0 3.275 3.948 -0.921



3KS : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O7 C2 O C doub 1.21 N N
2 N2 C13 N C sing 1.47 N N
3 O8 C15 O C doub 1.21 N N
4 C13 C12 C C sing 1.53 N N
5 C13 C14 C C sing 1.51 N N
6 C12 C11 C C sing 1.53 N N
7 C2 N C N sing 1.35 N N
8 C2 C1 C C sing 1.51 N N
9 O3 C9 O C doub 1.21 N N
10 C C1 C C sing 1.53 N N
11 C10 C11 C C sing 1.53 N N
12 C10 C8 C C sing 1.53 N N
13 C15 C16 C C sing 1.51 N N
14 C15 N3 C N sing 1.35 N N
15 N C3 N C sing 1.47 N N
16 N1 C8 N C sing 1.46 N N
17 N1 C7 N C sing 1.35 N N
18 C1 N3 C N sing 1.46 N N
19 C9 C8 C C sing 1.51 N N
20 C9 O2 C O sing 1.34 N N
21 C14 O5 C O doub 1.21 N N
22 C14 O4 C O sing 1.34 N N
23 C6 C7 C C sing 1.51 N N
24 C6 C5 C C sing 1.53 N N
25 C7 O6 C O doub 1.21 N N
26 O1 C4 O C doub 1.21 N N
27 C3 C5 C C sing 1.53 N N
28 C3 C4 C C sing 1.51 N N
29 C4 O C O sing 1.34 N N
30 C16 H163 C H sing 1.09 N N
31 C16 H162 C H sing 1.09 N N
32 C16 H161 C H sing 1.09 N N
33 N3 H31 N H sing 0.97 N N
34 C1 H11 C H sing 1.09 N N
35 C HC1 C H sing 1.09 N N
36 C HC2 C H sing 1.09 N N
37 C HC3 C H sing 1.09 N N
38 N HN1 N H sing 0.97 N N
39 C3 H32 C H sing 1.09 N N
40 O H1 O H sing 0.97 N N
41 C5 H51 C H sing 1.09 N N
42 C5 H52 C H sing 1.09 N N
43 C6 H62 C H sing 1.09 N N
44 C6 H61 C H sing 1.09 N N
45 N1 H12 N H sing 0.97 N N
46 C8 H81 C H sing 1.09 N N
47 O2 H2 O H sing 0.97 N N
48 C10 H101 C H sing 1.09 N N
49 C10 H102 C H sing 1.09 N N
50 C11 H111 C H sing 1.09 N N
51 C11 H112 C H sing 1.09 N N
52 C12 H121 C H sing 1.09 N N
53 C12 H122 C H sing 1.09 N N
54 C13 H131 C H sing 1.09 N N
55 N2 H22 N H sing 1.01 N N
56 N2 H21 N H sing 1.01 N N
57 O4 H4 O H sing 0.97 N N



3KS : Used in PDB Entries

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