Chemical Components in the PDB

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1NJ : Summary

Code

1NJ

One-letter code

X

Molecule name

2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid
OpenEye OEToolkits 1.7.6 2-[2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxy-pyridin-3-yl]-5-[[(2S)-3,3-dimethyl-1-oxidanyl-butan-2-yl]carbamoyl]benzoic acid

Formula

C28 H31 N5 O6

Formal charge

0

Molecular weight

533.576 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)c3c(c1c(nc(OC)cc1)C(=O)Nc2ccc(C(=[N@H])N)cc2)ccc(C(=O)NC(C(C)(C)C)CO)c3
SMILES CACTVS 3.370 COc1ccc(c2ccc(cc2C(O)=O)C(=O)N[CH](CO)C(C)(C)C)c(n1)C(=O)Nc3ccc(cc3)C(N)=N
SMILES OpenEye OEToolkits 1.7.6 CC(C)(C)C(CO)NC(=O)c1ccc(c(c1)C(=O)O)c2ccc(nc2C(=O)Nc3ccc(cc3)C(=N)N)OC
Canonical SMILES CACTVS 3.370 COc1ccc(c2ccc(cc2C(O)=O)C(=O)N[C@H](CO)C(C)(C)C)c(n1)C(=O)Nc3ccc(cc3)C(N)=N
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C(\c1ccc(cc1)NC(=O)c2c(ccc(n2)OC)c3ccc(cc3C(=O)O)C(=O)N[C@H](CO)C(C)(C)C)/N

IUPAC InChI

InChI=1S/C28H31N5O6/c1-28(2,3)21(14-34)32-25(35)16-7-10-18(20(13-16)27(37)38)19-11-12-22(39-4)33-23(19)26(36)31-17-8-5-15(6-9-17)24(29)30/h5-13,21,34H,14H2,1-4H3,(H3,29,30)(H,31,36)(H,32,35)(H,37,38)/t21-/m1/s1

IUPAC InChI key

KPACBFJTZSMBKD-OAQYLSRUSA-N
1NJ

wwPDB Information

Atom count

70 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-04-05

Last modified at

2013-08-16

Status

Released

Obsoleted

Not Assigned



1NJ : Atoms of Molecule

Total Number of Atoms: 70
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C10 N Y N 0 -3.68 4.184 -0.23
2 C11 C C11 N N N 0 -3.717 5.658 -0.111
3 C17 C C17 N Y N 0 -2.854 3.435 0.611
4 C19 C C19 N Y N 0 -2.826 2.062 0.502
5 C2 C C2 N N N 0 -2.422 -0.631 -0.353
6 C21 C C21 N Y N 0 -2.405 -2.111 -0.376
7 C23 C C23 N Y N 0 -3.556 -4.098 -0.635
8 C25 C C25 N N N 0 -5.881 -3.916 -1.082
9 C29 C C29 N Y N 0 -2.399 -4.848 -0.425
10 C31 C C31 N Y N 0 -1.206 -4.199 -0.183
11 C33 C C33 N Y N 0 -1.2 -2.798 -0.161
12 C34 C C34 N Y N 0 0.053 -2.056 0.094
13 C35 C C35 N Y N 0 1.107 -2.13 -0.815
14 C37 C C37 N Y N 0 2.275 -1.439 -0.579
15 C39 C C39 N Y N 0 0.183 -1.266 1.255
16 C40 C C40 N N N 0 -0.931 -1.179 2.219
17 C44 C C44 N Y N 0 1.365 -0.571 1.488
18 C46 C C46 N Y N 0 2.413 -0.659 0.573
19 C47 C C47 N N N 0 3.669 0.079 0.817
20 C5 C C5 N Y N 0 -3.61 1.423 -0.452
21 C51 C C51 S N N 0 5.929 0.726 0.176
22 C53 C C53 N N N 0 5.789 2.158 -0.344
23 C58 C C58 N N N 0 7.08 0.03 -0.552
24 C59 C C59 N N N 0 8.351 0.871 -0.421
25 C6 C C6 N Y N 0 -4.434 2.166 -1.291
26 C63 C C63 N N N 0 7.315 -1.349 0.068
27 C67 C C67 N N N 0 6.725 -0.13 -2.032
28 C8 C C8 N Y N 0 -4.47 3.539 -1.183
29 H1 H H1 N N N 0 -4.381 -0.456 -0.794
30 H10 H H10 N N N 0 -5.718 -3.271 -1.945
31 H11 H H11 N N N 0 -6.75 -4.55 -1.261
32 H12 H H12 N N N 0 -2.437 -5.927 -0.449
33 H13 H H13 N N N 0 -0.296 -4.758 -0.017
34 H14 H H14 N N N 0 1.007 -2.731 -1.707
35 H15 H H15 N N N 0 3.088 -1.501 -1.287
36 H16 H H16 N N N 0 -1.561 -0.396 3.929
37 H17 H H17 N N N 0 1.471 0.036 2.375
38 H18 H H18 N N N 0 4.589 -0.55 -0.863
39 H19 H H19 N N N 0 6.136 0.747 1.246
40 H2 H H2 N N N 0 -5.046 1.667 -2.028
41 H20 H H20 N N N 0 4.938 2.639 0.139
42 H21 H H21 N N N 0 6.698 2.717 -0.119
43 H22 H H22 N N N 0 5.485 3.009 -2.157
44 H23 H H23 N N N 0 8.604 0.985 0.633
45 H24 H H24 N N N 0 9.171 0.375 -0.94
46 H25 H H25 N N N 0 8.184 1.854 -0.862
47 H26 H H26 N N N 0 6.41 -1.949 -0.026
48 H27 H H27 N N N 0 8.135 -1.846 -0.451
49 H28 H H28 N N N 0 7.568 -1.235 1.122
50 H29 H H29 N N N 0 6.782 0.84 -2.526
51 H3 H H3 N N N 0 -5.11 4.116 -1.834
52 H30 H H30 N N N 0 7.427 -0.819 -2.501
53 H31 H H31 N N N 0 5.713 -0.526 -2.122
54 H4 H H4 N N N 0 -2.362 5.774 1.414
55 H5 H H5 N N N 0 -2.96 7.26 0.908
56 H6 H H6 N N N 0 -4.513 7.322 -0.818
57 H7 H H7 N N N 0 -2.241 3.932 1.348
58 H8 H H8 N N N 0 -2.19 1.482 1.155
59 H9 H H9 N N N 0 -6.056 -3.303 -0.198
60 N12 N N12 N N N 0 -2.936 6.293 0.83
61 N15 N N15 N N N 0 -4.489 6.356 -0.896
62 N22 N N22 N Y N 0 -3.528 -2.779 -0.605
63 N3 N N3 N N N 0 -3.575 0.033 -0.564
64 N49 N N49 N N N 0 4.683 -0.0050 -0.066
65 O1 O O1 N N N 0 -1.395 -0.015 -0.148
66 O24 O O24 N N N 0 -4.729 -4.735 -0.874
67 O41 O O41 N N N 0 -1.962 -1.787 2.013
68 O43 O O43 N N N 0 -0.804 -0.423 3.327
69 O48 O O48 N N N 0 3.789 0.763 1.816
70 O56 O O56 N N N 0 5.583 2.134 -1.758



1NJ : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O56 C53 O C sing 1.43 N N
2 C53 C51 C C sing 1.53 N N
3 O41 C40 O C doub 1.21 N N
4 C63 C58 C C sing 1.53 N N
5 C29 C31 C C doub 1.38 N Y
6 C29 C23 C C sing 1.39 N Y
7 C31 C33 C C sing 1.4 N Y
8 C51 N49 C N sing 1.46 N N
9 C51 C58 C C sing 1.53 N N
10 N49 C47 N C sing 1.35 N N
11 O24 C23 O C sing 1.36 N N
12 O24 C25 O C sing 1.43 N N
13 C40 C39 C C sing 1.48 N N
14 C40 O43 C O sing 1.35 N N
15 C58 C67 C C sing 1.53 N N
16 C58 C59 C C sing 1.53 N N
17 C23 N22 C N doub 1.32 N Y
18 C39 C44 C C doub 1.39 N Y
19 C39 C34 C C sing 1.41 N Y
20 C33 C34 C C sing 1.48 N N
21 C33 C21 C C doub 1.4 N Y
22 C44 C46 C C sing 1.39 N Y
23 C34 C35 C C doub 1.39 N Y
24 C46 C47 C C sing 1.48 N N
25 C46 C37 C C doub 1.4 N Y
26 C47 O48 C O doub 1.22 N N
27 C35 C37 C C sing 1.38 N Y
28 N22 C21 N C sing 1.33 N Y
29 C21 C2 C C sing 1.48 N N
30 C2 N3 C N sing 1.35 N N
31 C2 O1 C O doub 1.21 N N
32 N3 C5 N C sing 1.39 N N
33 C19 C5 C C doub 1.39 N Y
34 C19 C17 C C sing 1.38 N Y
35 C5 C6 C C sing 1.39 N Y
36 C17 C10 C C doub 1.4 N Y
37 C6 C8 C C doub 1.38 N Y
38 C10 C8 C C sing 1.4 N Y
39 C10 C11 C C sing 1.48 N N
40 N15 C11 N C doub 1.3 N N
41 C11 N12 C N sing 1.38 N N
42 N3 H1 N H sing 0.97 N N
43 C6 H2 C H sing 1.08 N N
44 C8 H3 C H sing 1.08 N N
45 N12 H4 N H sing 0.97 N N
46 N12 H5 N H sing 0.97 N N
47 N15 H6 N H sing 0.97 N N
48 C17 H7 C H sing 1.08 N N
49 C19 H8 C H sing 1.08 N N
50 C25 H9 C H sing 1.09 N N
51 C25 H10 C H sing 1.09 N N
52 C25 H11 C H sing 1.09 N N
53 C29 H12 C H sing 1.08 N N
54 C31 H13 C H sing 1.08 N N
55 C35 H14 C H sing 1.08 N N
56 C37 H15 C H sing 1.08 N N
57 O43 H16 O H sing 0.97 N N
58 C44 H17 C H sing 1.08 N N
59 N49 H18 N H sing 0.97 N N
60 C51 H19 C H sing 1.09 N N
61 C53 H20 C H sing 1.09 N N
62 C53 H21 C H sing 1.09 N N
63 O56 H22 O H sing 0.97 N N
64 C59 H23 C H sing 1.09 N N
65 C59 H24 C H sing 1.09 N N
66 C59 H25 C H sing 1.09 N N
67 C63 H26 C H sing 1.09 N N
68 C63 H27 C H sing 1.09 N N
69 C63 H28 C H sing 1.09 N N
70 C67 H29 C H sing 1.09 N N
71 C67 H30 C H sing 1.09 N N
72 C67 H31 C H sing 1.09 N N



1NJ : Used in PDB Entries

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