Chemical Components in the PDB

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DNS : Summary

Code

DNS

One-letter code

K

Molecule name

N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 N~6~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-lysine
OpenEye OEToolkits 1.5.0 (2S)-2-amino-6-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]hexanoic acid

Formula

C18 H25 N3 O4 S

Formal charge

0

Molecular weight

379.474 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N)CCCCNS(=O)(=O)c1cccc2c1cccc2N(C)C
SMILES CACTVS 3.341 CN(C)c1cccc2c1cccc2[S](=O)(=O)NCCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CN(C)c1cccc2c1cccc2S(=O)(=O)NCCCCC(C(=O)O)N
Canonical SMILES CACTVS 3.341 CN(C)c1cccc2c1cccc2[S](=O)(=O)NCCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CN(C)c1cccc2c1cccc2S(=O)(=O)NCCCC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C18H25N3O4S/c1-21(2)16-10-5-8-14-13(16)7-6-11-17(14)26(24,25)20-12-4-3-9-15(19)18(22)23/h5-8,10-11,15,20H,3-4,9,12,19H2,1-2H3,(H,22,23)/t15-/m0/s1

IUPAC InChI key

VQPRNSWQIAHPMS-HNNXBMFYSA-N
DNS

wwPDB Information

Atom count

51 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

2005-02-22

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



DNS : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 4.31 -3.814 0.23
2 N1 N N1 N N N 0 4.912 -2.488 0.422
3 C2 C C2 N N N 0 6.184 -2.492 -0.313
4 C3 C C3 N Y N 0 4.08 -1.575 -0.223
5 C4 C C4 N Y N 0 3.845 -1.682 -1.577
6 C5 C C5 N Y N 0 3.016 -0.775 -2.229
7 C6 C C6 N Y N 0 2.417 0.243 -1.552
8 C7 C C7 N Y N 0 2.63 0.388 -0.171
9 C8 C C8 N Y N 0 2.024 1.429 0.554
10 S S S N N N 0 0.979 2.587 -0.265
11 OA O OA N N N 0 1.697 3.006 -1.417
12 OB O OB N N N 0 0.483 3.446 0.752
13 NZ N NZ N N N 0 -0.335 1.755 -0.832
14 CE C CE N N N 0 -1.26 1.117 0.109
15 CD C CD N N N 0 -2.566 0.777 -0.611
16 CG C CG N N N 0 -3.532 0.112 0.371
17 CB C CB N N N 0 -4.838 -0.229 -0.349
18 CA C CA S N N 0 -5.804 -0.894 0.633
19 C C C N N N 0 -7.133 -1.118 -0.042
20 OXT O O N N Y 0 -8.004 -0.104 -0.16
21 O O OXT N N N 0 -7.413 -2.21 -0.477
22 N N N N N N 0 -5.251 -2.185 1.066
23 C9 C C9 N Y N 0 2.255 1.542 1.891
24 C10 C C10 N Y N 0 3.079 0.636 2.556
25 C11 C C11 N Y N 0 3.678 -0.387 1.886
26 C12 C C12 N Y N 0 3.467 -0.533 0.506
27 H11A H 1H1 N N N 0 3.358 -3.861 0.76
28 H12 H 2H1 N N N 0 4.143 -3.988 -0.833
29 H13 H 3H1 N N N 0 4.981 -4.578 0.622
30 H21 H 1H2 N N N 0 6.006 -2.791 -1.346
31 H22 H 2H2 N N N 0 6.618 -1.493 -0.294
32 H23 H 3H2 N N N 0 6.872 -3.196 0.155
33 H4 H H4 N N N 0 4.309 -2.48 -2.138
34 H5 H H5 N N N 0 2.847 -0.879 -3.291
35 H6 H H6 N N N 0 1.777 0.938 -2.076
36 HZ H HNZ N N N 0 -0.493 1.689 -1.786
37 HE3 H 1HE N N N 0 -0.811 0.203 0.498
38 HE2 H 2HE N N N 0 -1.467 1.8 0.934
39 HD3 H 1HD N N N 0 -3.016 1.691 -1.0
40 HD2 H 2HD N N N 0 -2.359 0.095 -1.436
41 HG3 H 1HG N N N 0 -3.083 -0.802 0.76
42 HG2 H 2HG N N N 0 -3.739 0.794 1.196
43 HB3 H 1HB N N N 0 -5.288 0.685 -0.738
44 HB2 H 2HB N N N 0 -4.631 -0.911 -1.174
45 HA H HA N N N 0 -5.942 -0.249 1.501
46 HO H HO N N N 0 -8.857 -0.248 -0.593
47 H H 1HN N N N 0 -5.961 -2.632 1.626
48 H2 H 2HN N N Y 0 -5.141 -2.746 0.234
49 H9 H H9 N N N 0 1.791 2.345 2.445
50 H10 H H10 N N N 0 3.243 0.746 3.617
51 H11 H H11 N N N 0 4.314 -1.083 2.414



DNS : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N1 C N sing 1.47 N N
2 C1 H11A C H sing 1.09 N N
3 C1 H12 C H sing 1.09 N N
4 C1 H13 C H sing 1.09 N N
5 N1 C2 N C sing 1.47 N N
6 N1 C3 N C sing 1.39 N N
7 C2 H21 C H sing 1.09 N N
8 C2 H22 C H sing 1.09 N N
9 C2 H23 C H sing 1.09 N N
10 C3 C4 C C sing 1.38 N Y
11 C3 C12 C C doub 1.41 N Y
12 C4 C5 C C doub 1.39 N Y
13 C4 H4 C H sing 1.08 N N
14 C5 C6 C C sing 1.36 N Y
15 C5 H5 C H sing 1.08 N N
16 C6 C7 C C doub 1.4 N Y
17 C6 H6 C H sing 1.08 N N
18 C7 C8 C C sing 1.41 N Y
19 C7 C12 C C sing 1.42 N Y
20 C8 S C S sing 1.76 N N
21 C8 C9 C C doub 1.36 N Y
22 S OA S O doub 1.42 N N
23 S OB S O doub 1.42 N N
24 S NZ S N sing 1.66 N N
25 NZ CE N C sing 1.47 N N
26 NZ HZ N H sing 0.97 N N
27 CE CD C C sing 1.53 N N
28 CE HE3 C H sing 1.09 N N
29 CE HE2 C H sing 1.09 N N
30 CD CG C C sing 1.53 N N
31 CD HD3 C H sing 1.09 N N
32 CD HD2 C H sing 1.09 N N
33 CG CB C C sing 1.53 N N
34 CG HG3 C H sing 1.09 N N
35 CG HG2 C H sing 1.09 N N
36 CB CA C C sing 1.53 N N
37 CB HB3 C H sing 1.09 N N
38 CB HB2 C H sing 1.09 N N
39 CA C C C sing 1.51 N N
40 CA N C N sing 1.47 N N
41 CA HA C H sing 1.09 N N
42 C OXT C O sing 1.34 N N
43 C O C O doub 1.21 N N
44 OXT HO O H sing 0.97 N N
45 N H N H sing 1.01 N N
46 N H2 N H sing 1.01 N N
47 C9 C10 C C sing 1.39 N Y
48 C9 H9 C H sing 1.08 N N
49 C10 C11 C C doub 1.36 N Y
50 C10 H10 C H sing 1.08 N N
51 C11 C12 C C sing 1.4 N Y
52 C11 H11 C H sing 1.08 N N



DNS : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
DNS 1wz1 Open in New Window Bound ligand 1 1
DNS 2k6r Open in New Window Polymer component 1 1