Chemical Components in the PDB

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2NC : Summary

Code

2NC

One-letter code

X

Molecule name

N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide

Synonyms

p2/NC

Systematic names

ProgramVersionName
ACDLabs 12.01 N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
OpenEye OEToolkits 1.7.0 [[[(4S)-4-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S,3S)-2-[[(2S,3R)-2-acetamido-3-hydroxy-butanoyl]amino]-3-methyl-pentanoyl]amino]hexyl]amino]hexanoyl]amino]-5-azanyl-5-oxo-pentanoyl]amino]-5-azanyl-5-oxo-pentyl]amino]-azanyl-methylidene]azanium

Formula

C35 H68 N11 O8

Formal charge

1

Molecular weight

770.983 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC(C(=O)NC(CCCC)CNC(C(=O)NC(C(=O)NC(C(=O)N)CCCNC(=[NH2+])\\N)CCC(=O)N)CCCC)C(C)CC)C(NC(=O)C)C(O)C
SMILES CACTVS 3.385 CCCC[CH](CN[CH](CCCC)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=[NH2+])C(N)=O)NC(=O)[CH](NC(=O)[CH](NC(C)=O)[CH](C)O)[CH](C)CC
SMILES OpenEye OEToolkits 1.7.5 CCCCC(CNC(CCCC)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=[NH2+])N)C(=O)N)NC(=O)C(C(C)CC)NC(=O)C(C(C)O)NC(=O)C
Canonical SMILES CACTVS 3.385 CCCC[C@@H](CN[C@@H](CCCC)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=[NH2+])C(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](NC(C)=O)[C@@H](C)O)[C@@H](C)CC
Canonical SMILES OpenEye OEToolkits 1.7.5 CCCC[C@@H](CN[C@@H](CCCC)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CCCNC(=[NH2+])N)C(=O)N)NC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H]([C@@H](C)O)NC(=O)C

IUPAC InChI

InChI=1S/C35H67N11O8/c1-7-10-13-23(43-33(53)28(20(4)9-3)46-34(54)29(21(5)47)42-22(6)48)19-41-25(14-11-8-2)31(51)45-26(16-17-27(36)49)32(52)44-24(30(37)50)15-12-18-40-35(38)39/h20-21,23-26,28-29,41,47H,7-19H2,1-6H3,(H2,36,49)(H2,37,50)(H,42,48)(H,43,53)(H,44,52)(H,45,51)(H,46,54)(H4,38,39,40)/p+1/t20-,21+,23-,24-,25-,26-,28-,29-/m0/s1

IUPAC InChI key

MQPXOVRKKPPKFZ-QYKDHROSSA-O

Has sub-components

2A0 , ARG , NH2
2NC

wwPDB Information

Atom count

122 (54 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-03-24

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



2NC : Atoms of Molecule

Total Number of Atoms: 122
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C1 N N N 0 10.5 2.652 -0.404
2 O O O1 N N N 0 10.254 3.339 -1.373
3 CH3 C C2 N N N 0 11.785 2.855 0.357
4 N N N1 N N N 0 9.622 1.711 -0.0050
5 CA C C3 S N N 0 8.37 1.518 -0.741
6 C1 C C4 N N N 0 7.337 0.914 0.175
7 O1 O O2 N N N 0 7.618 0.669 1.329
8 CB C C5 R N N 0 8.614 0.579 -1.924
9 OG1 O O3 N N N 0 8.97 -0.717 -1.439
10 CG2 C C6 N N N 0 9.75 1.131 -2.787
11 N1 N N2 N N N 0 6.1 0.646 -0.288
12 CA1 C C7 S N N 0 5.095 0.059 0.602
13 C2 C C8 N N N 0 4.075 -0.69 -0.216
14 O2 O O5 N N N 0 4.177 -0.73 -1.424
15 CB1 C C9 S N N 0 4.4 1.171 1.39
16 CG1 C C10 N N N 0 3.718 2.135 0.418
17 CG21 C C11 N N N 0 5.436 1.931 2.221
18 CD1 C C12 N N N 0 2.92 3.175 1.207
19 N2 N N3 N N N 0 3.049 -1.316 0.394
20 CA2 C C13 S N N 0 2.058 -2.044 -0.401
21 C3 C C14 N N N 0 0.739 -2.117 0.371
22 CB2 C C15 N N N 0 2.566 -3.461 -0.677
23 CG C C16 N N N 0 3.817 -3.392 -1.555
24 CD C C17 N N N 0 4.326 -4.808 -1.831
25 CE C C18 N N N 0 5.577 -4.739 -2.709
26 N3 N N4 N N N 0 0.312 -0.761 0.74
27 CA3 C C19 S N N 0 -0.909 -0.797 1.556
28 C4 C C20 N N N 0 -2.115 -0.829 0.654
29 O3 O O9 N N N 0 -1.972 -0.822 -0.55
30 CB3 C C21 N N N 0 -0.967 0.449 2.442
31 CG3 C C22 N N N 0 0.188 0.417 3.445
32 CD2 C C23 N N N 0 0.081 1.619 4.385
33 CE1 C C24 N N N 0 1.236 1.586 5.388
34 N4 N N5 N N N 0 -3.353 -0.865 1.185
35 CA4 C C25 S N N 0 -4.527 -0.896 0.308
36 C5 C C26 N N N 0 -5.716 -0.33 1.04
37 O4 O O11 N N N 0 -5.596 0.06 2.182
38 CB4 C C27 N N N 0 -4.819 -2.341 -0.101
39 CG4 C C28 N N N 0 -3.664 -2.874 -0.951
40 CD3 C C29 N N N 0 -3.953 -4.298 -1.354
41 OE1 O O12 N N N 0 -4.981 -4.832 -0.997
42 NE2 N N6 N N N 0 -3.068 -4.976 -2.111
43 N5 N N7 N N N 0 -6.914 -0.259 0.426
44 CA5 C C30 S N N 0 -8.07 0.291 1.138
45 C6 C C31 N N N 0 -8.718 -0.794 1.958
46 O5 O O14 N N N 0 -8.259 -1.917 1.949
47 CB5 C C32 N N N 0 -9.08 0.837 0.125
48 CG5 C C33 N N N 0 -8.463 2.021 -0.622
49 CD4 C C34 N N N 0 -9.473 2.567 -1.634
50 NE N N8 N N N 0 -8.883 3.701 -2.349
51 CZ C C35 N N N 0 -9.605 4.354 -3.31
52 NH1 N N9 N N N 0 -10.844 3.959 -3.595
53 NH2 N N10 N N N 1 -9.068 5.386 -3.96
54 N6 N N11 N N N 0 -9.807 -0.518 2.701
55 H1 H H2 N N N 0 11.628 3.59 1.146
56 H2 H H3 N N N 0 12.099 1.909 0.799
57 H3 H H4 N N N 0 12.558 3.212 -0.324
58 H H H5 N N N 0 9.818 1.161 0.77
59 HA H H7 N N N 0 8.012 2.48 -1.108
60 HB H H8 N N N 0 7.706 0.505 -2.523
61 HG1 H H9 N N N 0 9.771 -0.727 -0.896
62 HG21 H H10 N N N 0 10.658 1.204 -2.189
63 HG22 H H11 N N N 0 9.924 0.462 -3.63
64 HG23 H H12 N N N 0 9.478 2.119 -3.158
65 H4 H H14 N N N 0 5.874 0.842 -1.211
66 HA1 H H16 N N N 0 5.581 -0.628 1.295
67 HB1 H H17 N N N 0 3.653 0.734 2.052
68 HG12 H H18 N N N 0 4.474 2.638 -0.185
69 HG13 H H19 N N N 0 3.045 1.579 -0.234
70 HG24 H H20 N N N 0 4.94 2.723 2.782
71 HG25 H H21 N N N 0 5.921 1.244 2.913
72 HG26 H H22 N N N 0 6.183 2.368 1.558
73 HD11 H H23 N N N 0 2.434 3.862 0.514
74 HD12 H H24 N N N 0 2.164 2.672 1.809
75 HD13 H H25 N N N 0 3.593 3.732 1.859
76 H5 H H27 N N N 0 2.968 -1.285 1.36
77 HA2 H H29 N N N 0 1.898 -1.525 -1.346
78 HC31 H HC31 N N N 0 -0.024 -2.58 -0.256
79 HC32 H HC32 N N N 0 0.878 -2.712 1.273
80 HB2 H H31 N N N 0 2.81 -3.95 0.266
81 HB3 H H32 N N N 0 1.792 -4.031 -1.192
82 HG2 H H33 N N N 0 3.573 -2.903 -2.498
83 HG3 H H34 N N N 0 4.591 -2.822 -1.04
84 HD2 H H35 N N N 0 4.57 -5.297 -0.888
85 HD3 H H36 N N N 0 3.552 -5.378 -2.346
86 HE1 H H37 N N N 0 5.939 -5.748 -2.905
87 HE2 H H38 N N N 0 5.332 -4.251 -3.652
88 HE3 H H39 N N N 0 6.351 -4.169 -2.194
89 H6 H H40 N N N 0 0.182 -0.187 -0.08
90 HA3 H H42 N N N 0 -0.9 -1.688 2.183
91 HB21 H H44 N N N 0 -0.884 1.341 1.82
92 HB31 H H45 N N N 0 -1.915 0.469 2.98
93 HG27 H H46 N N N 0 0.139 -0.504 4.025
94 HG31 H H47 N N N 0 1.136 0.458 2.908
95 HD21 H H48 N N N 0 0.13 2.54 3.804
96 HD31 H H49 N N N 0 -0.867 1.577 4.921
97 HE11 H H50 N N N 0 1.187 0.665 5.969
98 HE21 H H51 N N N 0 2.184 1.628 4.852
99 HE31 H H52 N N N 0 1.16 2.443 6.058
100 H7 H H53 N N N 0 -3.468 -0.87 2.148
101 HA4 H H55 N N N 0 -4.33 -0.299 -0.582
102 HB22 H H56 N N N 0 -4.928 -2.957 0.792
103 HB32 H H57 N N N 0 -5.742 -2.375 -0.68
104 HG28 H H58 N N N 0 -3.556 -2.259 -1.844
105 HG32 H H59 N N N 0 -2.741 -2.841 -0.372
106 HE22 H H60 N N N 0 -2.246 -4.548 -2.397
107 HE23 H H61 N N N 0 -3.253 -5.892 -2.371
108 H8 H H63 N N N 0 -7.01 -0.571 -0.487
109 HA5 H H65 N N N 0 -7.743 1.097 1.795
110 HB23 H H66 N N N 0 -9.34 0.054 -0.587
111 HB33 H H67 N N N 0 -9.978 1.165 0.649
112 HG29 H H68 N N N 0 -8.203 2.805 0.091
113 HG33 H H69 N N N 0 -7.565 1.693 -1.145
114 HD22 H H70 N N N 0 -9.733 1.784 -2.346
115 HD32 H H71 N N N 0 -10.371 2.895 -1.11
116 HE H H72 N N N 0 -7.98 3.989 -2.141
117 HH11 H H73 N N N 0 -11.235 3.208 -3.121
118 HH12 H H74 N N N 0 -11.356 4.423 -4.276
119 HH21 H H75 N N N 0 -8.165 5.673 -3.752
120 HH22 H H76 N N N 0 -9.58 5.849 -4.641
121 HN1 H H78 N N N 0 -10.175 0.38 2.708
122 HN2 H H79 N N N 0 -10.224 -1.217 3.229



2NC : Chemical Bonds

Total Number of Bonds: 121
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C O C O doub 1.21 N N
2 C CH3 C C sing 1.51 N N
3 CH3 H1 C H sing 1.09 N N
4 CH3 H2 C H sing 1.09 N N
5 CH3 H3 C H sing 1.09 N N
6 N CA N C sing 1.47 N N
7 N H N H sing 0.97 N N
8 CA C1 C C sing 1.51 N N
9 CA CB C C sing 1.53 N N
10 CA HA C H sing 1.09 N N
11 C1 O1 C O doub 1.21 N N
12 CB OG1 C O sing 1.43 N N
13 CB CG2 C C sing 1.53 N N
14 CB HB C H sing 1.09 N N
15 OG1 HG1 O H sing 0.97 N N
16 CG2 HG21 C H sing 1.09 N N
17 CG2 HG22 C H sing 1.09 N N
18 CG2 HG23 C H sing 1.09 N N
19 N1 CA1 N C sing 1.47 N N
20 N1 H4 N H sing 0.97 N N
21 CA1 C2 C C sing 1.51 N N
22 CA1 CB1 C C sing 1.53 N N
23 CA1 HA1 C H sing 1.09 N N
24 C2 O2 C O doub 1.21 N N
25 CB1 CG1 C C sing 1.53 N N
26 CB1 CG21 C C sing 1.53 N N
27 CB1 HB1 C H sing 1.09 N N
28 CG1 CD1 C C sing 1.53 N N
29 CG1 HG12 C H sing 1.09 N N
30 CG1 HG13 C H sing 1.09 N N
31 CG21 HG24 C H sing 1.09 N N
32 CG21 HG25 C H sing 1.09 N N
33 CG21 HG26 C H sing 1.09 N N
34 CD1 HD11 C H sing 1.09 N N
35 CD1 HD12 C H sing 1.09 N N
36 CD1 HD13 C H sing 1.09 N N
37 N2 CA2 N C sing 1.46 N N
38 N2 H5 N H sing 0.97 N N
39 CA2 C3 C C sing 1.53 N N
40 CA2 CB2 C C sing 1.53 N N
41 CA2 HA2 C H sing 1.09 N N
42 CB2 CG C C sing 1.53 N N
43 CB2 HB2 C H sing 1.09 N N
44 CB2 HB3 C H sing 1.09 N N
45 CG CD C C sing 1.53 N N
46 CG HG2 C H sing 1.09 N N
47 CG HG3 C H sing 1.09 N N
48 CD CE C C sing 1.53 N N
49 CD HD2 C H sing 1.09 N N
50 CD HD3 C H sing 1.09 N N
51 CE HE1 C H sing 1.09 N N
52 CE HE2 C H sing 1.09 N N
53 CE HE3 C H sing 1.09 N N
54 N3 CA3 N C sing 1.47 N N
55 N3 H6 N H sing 1.01 N N
56 CA3 C4 C C sing 1.51 N N
57 CA3 CB3 C C sing 1.53 N N
58 CA3 HA3 C H sing 1.09 N N
59 C4 O3 C O doub 1.21 N N
60 CB3 CG3 C C sing 1.53 N N
61 CB3 HB21 C H sing 1.09 N N
62 CB3 HB31 C H sing 1.09 N N
63 CG3 CD2 C C sing 1.53 N N
64 CG3 HG27 C H sing 1.09 N N
65 CG3 HG31 C H sing 1.09 N N
66 CD2 CE1 C C sing 1.53 N N
67 CD2 HD21 C H sing 1.09 N N
68 CD2 HD31 C H sing 1.09 N N
69 CE1 HE11 C H sing 1.09 N N
70 CE1 HE21 C H sing 1.09 N N
71 CE1 HE31 C H sing 1.09 N N
72 N4 CA4 N C sing 1.47 N N
73 N4 H7 N H sing 0.97 N N
74 CA4 C5 C C sing 1.51 N N
75 CA4 CB4 C C sing 1.53 N N
76 CA4 HA4 C H sing 1.09 N N
77 C5 O4 C O doub 1.21 N N
78 CB4 CG4 C C sing 1.53 N N
79 CB4 HB22 C H sing 1.09 N N
80 CB4 HB32 C H sing 1.09 N N
81 CG4 CD3 C C sing 1.51 N N
82 CG4 HG28 C H sing 1.09 N N
83 CG4 HG32 C H sing 1.09 N N
84 CD3 OE1 C O doub 1.21 N N
85 CD3 NE2 C N sing 1.35 N N
86 NE2 HE22 N H sing 0.97 N N
87 NE2 HE23 N H sing 0.97 N N
88 N5 CA5 N C sing 1.46 N N
89 N5 H8 N H sing 0.97 N N
90 CA5 C6 C C sing 1.51 N N
91 CA5 CB5 C C sing 1.53 N N
92 CA5 HA5 C H sing 1.09 N N
93 C6 O5 C O doub 1.21 N N
94 CB5 CG5 C C sing 1.53 N N
95 CB5 HB23 C H sing 1.09 N N
96 CB5 HB33 C H sing 1.09 N N
97 CG5 CD4 C C sing 1.53 N N
98 CG5 HG29 C H sing 1.09 N N
99 CG5 HG33 C H sing 1.09 N N
100 CD4 NE C N sing 1.46 N N
101 CD4 HD22 C H sing 1.09 N N
102 CD4 HD32 C H sing 1.09 N N
103 NE CZ N C sing 1.37 N N
104 NE HE N H sing 0.97 N N
105 CZ NH1 C N sing 1.33 N N
106 CZ NH2 C N doub 1.33 N N
107 NH1 HH11 N H sing 0.97 N N
108 NH1 HH12 N H sing 0.97 N N
109 NH2 HH21 N H sing 0.97 N N
110 NH2 HH22 N H sing 0.97 N N
111 N6 HN1 N H sing 0.97 N N
112 N6 HN2 N H sing 0.97 N N
113 C N C N sing 1.35 N N
114 C1 N1 C N sing 1.35 N N
115 C2 N2 C N sing 1.35 N N
116 C3 N3 C N sing 1.47 N N
117 C4 N4 C N sing 1.35 N N
118 C5 N5 C N sing 1.35 N N
119 C3 HC31 C H sing 1.09 N N
120 C3 HC32 C H sing 1.09 N N
121 C6 N6 C N sing 1.35 N N



2NC : Used in PDB Entries

Total Number of PDB Entries: 31
Ligand Code PDB Entry ID Type Total Distinct
2NC 1fej Open in New Window Bound ligand 1 1
2NC 1ff0 Open in New Window Bound ligand 1 1
2NC 1ffi Open in New Window Bound ligand 1 1
2NC 1fg6 Open in New Window Bound ligand 1 1
2NC 1fgc Open in New Window Bound ligand 1 1
2NC 2aoc Open in New Window Bound ligand 1 1
2NC 2aod Open in New Window Bound ligand 1 1
2NC 2aog Open in New Window Bound ligand 1 1
2NC 2avm Open in New Window Bound ligand 1 1
2NC 2avq Open in New Window Bound ligand 1 1
2NC 2j9k Open in New Window Bound ligand 1 1
2NC 2o40 Open in New Window Bound ligand 1 1
2NC 3bva Open in New Window Bound ligand 1 1
2NC 3fsm Open in New Window Bound ligand 1 1
2NC 3hau Open in New Window Bound ligand 1 1
2NC 3haw Open in New Window Bound ligand 1 1
2NC 3hbo Open in New Window Bound ligand 1 1
2NC 3hdk Open in New Window Bound ligand 1 1
2NC 3hlo Open in New Window Bound ligand 1 1
2NC 3hzc Open in New Window Bound ligand 1 1
2NC 3i2l Open in New Window Bound ligand 1 1
2NC 3ia9 Open in New Window Bound ligand 1 1
2NC 3iaw Open in New Window Bound ligand 1 1
2NC 3ka2 Open in New Window Bound ligand 1 1
2NC 3nwq Open in New Window Bound ligand 1 1
2NC 3nxe Open in New Window Bound ligand 1 1
2NC 3nyg Open in New Window Bound ligand 1 1
2NC 3uhl Open in New Window Bound ligand 1 1
2NC 4hvp Open in New Window Bound ligand 1 1
2NC 6o57 Open in New Window Bound ligand 1 1
2NC 6o5a Open in New Window Bound ligand 1 1