Chemical Components in the PDB

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8UX : Summary

Code

8UX

One-letter code

X

Molecule name

(2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid

Synonyms

staphylopine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid

Formula

C13 H20 N4 O6

Formal charge

0

Molecular weight

328.321 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](N[CH](CCN[CH](Cc1c[nH]cn1)C(O)=O)C(O)=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 CC(C(=O)O)NC(CCNC(Cc1c[nH]cn1)C(=O)O)C(=O)O
Canonical SMILES CACTVS 3.385 C[C@H](N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(O)=O)C(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@@H](C(=O)O)N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C13H20N4O6/c1-7(11(18)19)17-9(12(20)21)2-3-15-10(13(22)23)4-8-5-14-6-16-8/h5-7,9-10,15,17H,2-4H2,1H3,(H,14,16)(H,18,19)(H,20,21)(H,22,23)/t7-,9-,10+/m0/s1

IUPAC InChI key

WLNNYKMTYVPSDL-UJNFCWOMSA-N
8UX

wwPDB Information

Atom count

43 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-09-28

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



8UX : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O O O1 N N N 0 -4.87 -2.007 1.88
2 C C C1 N N N 0 -3.99 -1.612 0.947
3 OXT O O2 N N N 0 -3.47 -2.427 0.222
4 CA C C2 S N N 0 -3.652 -0.15 0.802
5 CB C C3 N N N 0 -4.921 0.637 0.471
6 N N N1 N N N 0 -2.673 0.021 -0.28
7 CAV C C4 S N N 0 -1.887 1.247 -0.09
8 CAR C C5 N N N 0 -2.636 2.419 -0.669
9 OAF O O3 N N N 0 -2.105 3.651 -0.609
10 OAC O O4 N N N 0 -3.714 2.251 -1.187
11 CAK C C6 N N N 0 -0.539 1.103 -0.798
12 CAJ C C7 N N N 0 0.274 -0.0070 -0.128
13 NAN N N2 N N N 0 1.568 -0.145 -0.808
14 CAW C C8 R N N 0 2.377 -1.204 -0.19
15 CAS C C9 N N N 0 1.997 -2.537 -0.782
16 OAG O O5 N N N 0 2.61 -3.656 -0.366
17 OAD O O6 N N N 0 1.14 -2.598 -1.632
18 CAL C C10 N N N 0 3.86 -0.933 -0.454
19 CAT C C11 N Y N 0 4.27 0.339 0.243
20 CAI C C12 N Y N 0 5.286 0.471 1.117
21 NAM N N3 N Y N 0 5.307 1.783 1.504
22 CAH C C13 N Y N 0 4.303 2.409 0.852
23 NAP N N4 N Y N 0 3.69 1.54 0.096
24 H1 H H1 N N N 0 -5.055 -2.955 1.935
25 H2 H H2 N N N 0 -3.229 0.219 1.736
26 H3 H H3 N N N 0 -5.345 0.268 -0.463
27 H4 H H4 N N N 0 -5.647 0.51 1.274
28 H5 H H5 N N N 0 -4.676 1.694 0.367
29 H6 H H6 N N N 0 -3.127 0.019 -1.181
30 H8 H H8 N N N 0 -1.722 1.411 0.975
31 H9 H H9 N N N 0 -2.623 4.371 -0.994
32 H10 H H10 N N N 0 -0.703 0.851 -1.846
33 H11 H H11 N N N 0 0.0080 2.044 -0.733
34 H12 H H12 N N N 0 0.439 0.245 0.92
35 H13 H H13 N N N 0 -0.273 -0.947 -0.193
36 H14 H H14 N N N 0 2.067 0.732 -0.817
37 H16 H H16 N N N 0 2.196 -1.219 0.885
38 H17 H H17 N N N 0 2.333 -4.487 -0.775
39 H18 H H18 N N N 0 4.454 -1.764 -0.073
40 H19 H H19 N N N 0 4.025 -0.83 -1.526
41 H20 H H20 N N N 0 5.955 -0.31 1.449
42 H21 H H21 N N N 0 5.928 2.189 2.129
43 H22 H H22 N N N 0 4.052 3.455 0.94



8UX : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAI NAM C N sing 1.37 N Y
2 CAI CAT C C doub 1.35 N Y
3 CAL CAT C C sing 1.51 N N
4 CAL CAW C C sing 1.53 N N
5 NAM CAH N C sing 1.35 N Y
6 CAT NAP C N sing 1.34 N Y
7 CAW NAN C N sing 1.47 N N
8 CAW CAS C C sing 1.51 N N
9 CAH NAP C N doub 1.3 N Y
10 NAN CAJ N C sing 1.47 N N
11 OAD CAS O C doub 1.21 N N
12 CAS OAG C O sing 1.34 N N
13 CAJ CAK C C sing 1.53 N N
14 OAC CAR O C doub 1.21 N N
15 CAK CAV C C sing 1.53 N N
16 OAF CAR O C sing 1.34 N N
17 CAR CAV C C sing 1.51 N N
18 CAV N C N sing 1.47 N N
19 OXT C O C doub 1.21 N N
20 N CA N C sing 1.47 N N
21 C CA C C sing 1.51 N N
22 C O C O sing 1.34 N N
23 CA CB C C sing 1.53 N N
24 O H1 O H sing 0.97 N N
25 CA H2 C H sing 1.09 N N
26 CB H3 C H sing 1.09 N N
27 CB H4 C H sing 1.09 N N
28 CB H5 C H sing 1.09 N N
29 N H6 N H sing 1.01 N N
30 CAV H8 C H sing 1.09 N N
31 OAF H9 O H sing 0.97 N N
32 CAK H10 C H sing 1.09 N N
33 CAK H11 C H sing 1.09 N N
34 CAJ H12 C H sing 1.09 N N
35 CAJ H13 C H sing 1.09 N N
36 NAN H14 N H sing 1.01 N N
37 CAW H16 C H sing 1.09 N N
38 OAG H17 O H sing 0.97 N N
39 CAL H18 C H sing 1.09 N N
40 CAL H19 C H sing 1.09 N N
41 CAI H20 C H sing 1.08 N N
42 NAM H21 N H sing 0.97 N N
43 CAH H22 C H sing 1.08 N N



8UX : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
8UX 5yh8 Open in New Window Bound ligand 1 1
8UX 5yhe Open in New Window Bound ligand 2 1
8UX 5yhg Open in New Window Bound ligand 1 1
8UX 6h3f Open in New Window Bound ligand 1 1