Chemical Components in the PDB

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E13 : Summary

Code

E13

One-letter code

X

Molecule name

N-[(2S,3S)-4-{(4R)-4-[(2,2-dimethylpropyl)carbamoyl]-5,5-dimethyl-1,3-thiazolidin-3-yl}-3-hydroxy-4-oxo-1-phenylbutan-2-yl]-N~2~-{(2S)-2-[(methoxycarbonyl)amino]-2-phenylacetyl}-3-methyl-L-valinamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(2S,3S)-4-{(4R)-4-[(2,2-dimethylpropyl)carbamoyl]-5,5-dimethyl-1,3-thiazolidin-3-yl}-3-hydroxy-4-oxo-1-phenylbutan-2-yl]-N~2~-{(2S)-2-[(methoxycarbonyl)amino]-2-phenylacetyl}-3-methyl-L-valinamide
OpenEye OEToolkits 1.7.0 methyl N-[(1S)-2-[[(2S)-1-[[(2S,3S)-4-[(4R)-4-(2,2-dimethylpropylcarbamoyl)-5,5-dimethyl-1,3-thiazolidin-3-yl]-3-hydroxy-4-oxo-1-phenyl-butan-2-yl]amino]-3,3-dimethyl-1-oxo-butan-2-yl]amino]-2-oxo-1-phenyl-ethyl]carbamate

Formula

C37 H53 N5 O7 S

Formal charge

0

Molecular weight

711.911 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCC(C)(C)C)C3N(C(=O)C(O)C(NC(=O)C(NC(=O)C(c1ccccc1)NC(=O)OC)C(C)(C)C)Cc2ccccc2)CSC3(C)C
SMILES CACTVS 3.370 COC(=O)N[CH](C(=O)N[CH](C(=O)N[CH](Cc1ccccc1)[CH](O)C(=O)N2CSC(C)(C)[CH]2C(=O)NCC(C)(C)C)C(C)(C)C)c3ccccc3
SMILES OpenEye OEToolkits 1.7.0 CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)C(C(C)(C)C)NC(=O)C(c3ccccc3)NC(=O)OC)O)C(=O)NCC(C)(C)C)C
Canonical SMILES CACTVS 3.370 COC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](Cc1ccccc1)[C@H](O)C(=O)N2CSC(C)(C)[C@H]2C(=O)NCC(C)(C)C)C(C)(C)C)c3ccccc3
Canonical SMILES OpenEye OEToolkits 1.7.0 CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)[C@H](C(C)(C)C)NC(=O)[C@H](c3ccccc3)NC(=O)OC)O)C(=O)NCC(C)(C)C)C

IUPAC InChI

InChI=1S/C37H53N5O7S/c1-35(2,3)21-38-32(46)29-37(7,8)50-22-42(29)33(47)27(43)25(20-23-16-12-10-13-17-23)39-31(45)28(36(4,5)6)41-30(44)26(40-34(48)49-9)24-18-14-11-15-19-24/h10-19,25-29,43H,20-22H2,1-9H3,(H,38,46)(H,39,45)(H,40,48)(H,41,44)/t25-,26-,27-,28+,29+/m0/s1

IUPAC InChI key

BNMOFZILPSBXGG-OTJWULCMSA-N

Has sub-components

000 , 004
E13

wwPDB Information

Atom count

103 (50 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-02-05

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



E13 : Atoms of Molecule

Total Number of Atoms: 103
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CB1 C C N N N 0 -8.387 0.008 -0.618
2 OA1 O O N N N 0 -8.283 0.255 -1.803
3 OA2 O OA N N N 0 -9.607 -0.113 -0.061
4 CB2 C CB N N N 0 -10.752 0.07 -0.935
5 CBF C C1 N N N 0 -4.956 -0.807 0.342
6 NAJ N N N N N 0 -7.283 -0.15 0.138
7 OAK O O1 N N N 0 -5.316 -1.411 1.33
8 CBM C CA S N N 0 -5.956 -0.024 -0.469
9 CBK C CB1 N Y N 0 -5.552 1.428 -0.499
10 CAQ C CE N Y N 0 -4.812 4.091 -0.553
11 CAT C CD1 N Y N 0 -4.527 3.272 -1.63
12 CAU C CD2 N Y N 0 -5.472 3.579 0.549
13 CAX C CG1 N Y N 0 -4.897 1.941 -1.603
14 CAY C CG2 N Y N 0 -5.842 2.247 0.576
15 N N N1 N N N 0 -3.661 -0.836 -0.031
16 CA C CA1 S N N 0 -2.689 -1.598 0.758
17 CB C CB2 N N N 0 -2.7 -3.06 0.308
18 CAG C CG11 N N N 0 -2.175 -3.155 -1.127
19 CG1 C CG21 N N N 0 -1.805 -3.885 1.234
20 CG2 C CG3 N N N 0 -4.13 -3.601 0.365
21 C C C2 N N N 0 -1.312 -1.019 0.553
22 O O O2 N N N 0 -1.128 -0.181 -0.304
23 CBI C C3 N N N 0 3.479 -1.483 1.224
24 NBC N N2 N N N 0 -0.286 -1.433 1.323
25 OAN O O3 N N N 0 4.188 -0.965 2.06
26 CBN C CA2 S N N 0 2.091 -1.941 1.592
27 CBJ C CD N Y N 0 0.331 1.435 1.196
28 CBA C CG N N N 0 1.256 0.406 1.793
29 CAP C CH N Y N 0 -1.366 3.323 0.101
30 CBO C CB11 S N N 0 1.067 -0.93 1.071
31 OAO O OB2 N N N 0 1.983 -2.04 3.013
32 CAV C CE1 N Y N 0 -0.941 1.602 1.711
33 CAW C CE2 N Y N 0 0.757 2.216 0.138
34 CAR C CZ1 N Y N 0 -1.79 2.545 1.163
35 CAS C CZ2 N Y N 0 -0.091 3.161 -0.409
36 CBH C C4 N N N 0 5.537 0.144 -0.124
37 NBR N N3 N N N 0 3.933 -1.65 -0.034
38 OAM O O4 N N N 0 4.598 0.894 0.041
39 CBQ C CA3 R N N 0 5.293 -1.313 -0.424
40 CBU C CB3 N N N 0 5.576 -1.565 -1.923
41 CAZ C CD3 N N N 0 3.087 -2.194 -1.115
42 CAH C CG12 N N N 0 6.459 -0.461 -2.509
43 CAI C CG22 N N N 0 6.207 -2.942 -2.139
44 CBS C C21 N N N 0 8.54 2.296 0.296
45 SBE S SG3 N N N 0 3.876 -1.498 -2.628
46 NBB N N4 N N N 0 6.797 0.613 -0.038
47 CBL C C11 N N N 0 7.034 2.029 0.254
48 CAB C C31 N N N 0 9.158 1.945 -1.059
49 CAC C C41 N N N 0 8.787 3.775 0.601
50 CAD C C5 N N N 0 9.181 1.436 1.387
51 HB2 H HB N N N 0 -10.721 -0.669 -1.735
52 HB2A H HBA N N N 0 -11.671 -0.054 -0.361
53 HB2B H HBB N N N 0 -10.725 1.072 -1.365
54 HNAJ H HN N N N 0 -7.367 -0.347 1.084
55 HBM H HA N N N 0 -5.983 -0.414 -1.487
56 HAQ H HE N N N 0 -4.519 5.13 -0.572
57 HAT H HD1 N N N 0 -4.012 3.672 -2.49
58 HAU H HD2 N N N 0 -5.695 4.219 1.39
59 HAX H HG1 N N N 0 -4.674 1.301 -2.444
60 HAY H HG2 N N N 0 -6.358 1.848 1.436
61 HN H HN1 N N N 0 -3.372 -0.354 -0.821
62 HA H HA1 N N N 0 -2.953 -1.541 1.814
63 HAG H HG11 N N N 0 -1.156 -2.77 -1.167
64 HAGA H HG12 N N N 0 -2.183 -4.197 -1.447
65 HAGB H HG13 N N N 0 -2.813 -2.567 -1.786
66 HG1 H HG21 N N N 0 -2.185 -3.827 2.254
67 HG2A H HG32 N N N 0 -4.137 -4.642 0.044
68 HG1A H HG22 N N N 0 -1.803 -4.925 0.906
69 HG1B H HG23 N N N 0 -0.789 -3.492 1.203
70 HG2 H HG31 N N N 0 -4.767 -3.012 -0.295
71 HG2B H HG33 N N N 0 -4.503 -3.532 1.387
72 HNBC H HN2 N N N 0 -0.443 -2.064 2.042
73 HBN H HA2 N N N 0 1.899 -2.915 1.143
74 HBA H HG N N N 0 2.289 0.736 1.68
75 HBAA H HGA N N N 0 1.028 0.282 2.852
76 HAP H HH N N N 0 -2.029 4.06 -0.327
77 HBO H HB1 N N N 0 1.208 -0.787 0.0
78 HOAO H HOB2 N N N 0 2.142 -1.207 3.479
79 HAV H HE1 N N N 0 -1.272 0.994 2.54
80 HAW H HE2 N N N 0 1.753 2.089 -0.26
81 HAR H HZ1 N N N 0 -2.786 2.672 1.561
82 HAS H HZ2 N N N 0 0.24 3.768 -1.238
83 HBQ H HA3 N N N 0 5.986 -1.912 0.167
84 HAZ H HD N N N 0 3.124 -3.284 -1.123
85 HAZA H HDA N N N 0 2.06 -1.844 -1.015
86 HAH H HG14 N N N 0 7.409 -0.434 -1.974
87 HAHA H HG1A N N N 0 6.642 -0.664 -3.564
88 HAHB H HG1B N N N 0 5.956 0.5 -2.405
89 HAI H HG24 N N N 0 5.528 -3.714 -1.777
90 HAIA H HG2A N N N 0 6.396 -3.093 -3.202
91 HAIB H HG2B N N N 0 7.148 -3.001 -1.591
92 HNBB H HN11 N N N 0 7.548 0.013 -0.17
93 HBL H H11 N N N 0 6.577 2.641 -0.523
94 HBLA H H12 N N N 0 6.594 2.279 1.219
95 HAB H H31 N N N 0 8.701 2.557 -1.836
96 HABA H H32 N N N 0 10.231 2.135 -1.029
97 HABB H H33 N N N 0 8.982 0.891 -1.276
98 HACB H H43 N N N 0 8.33 4.387 -0.176
99 HAC H H41 N N N 0 8.347 4.025 1.566
100 HACA H H42 N N N 0 9.859 3.965 0.631
101 HAD H H51 N N N 0 9.005 0.382 1.17
102 HADA H H52 N N N 0 10.253 1.627 1.417
103 HADB H H53 N N N 0 8.74 1.686 2.352



E13 : Chemical Bonds

Total Number of Bonds: 105
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OA1 CB1 O C doub 1.21 N N
2 OA2 CB1 O C sing 1.35 N N
3 CB2 OA2 C O sing 1.45 N N
4 CB2 HB2 C H sing 1.09 N N
5 CB2 HB2A C H sing 1.09 N N
6 CB2 HB2B C H sing 1.09 N N
7 CBF OAK C O doub 1.21 N N
8 NAJ HNAJ N H sing 0.97 N N
9 CBM CBF C C sing 1.51 N N
10 CBM NAJ C N sing 1.46 N N
11 CBM CBK C C sing 1.51 N N
12 CBM HBM C H sing 1.09 N N
13 CBK CAX C C sing 1.38 N Y
14 CAQ CAT C C sing 1.38 N Y
15 CAQ HAQ C H sing 1.08 N N
16 CAT HAT C H sing 1.08 N N
17 CAU CAQ C C doub 1.38 N Y
18 CAU HAU C H sing 1.08 N N
19 CAX CAT C C doub 1.38 N Y
20 CAX HAX C H sing 1.08 N N
21 CAY CBK C C doub 1.38 N Y
22 CAY CAU C C sing 1.38 N Y
23 CAY HAY C H sing 1.08 N N
24 N CA N C sing 1.47 N N
25 N HN N H sing 0.97 N N
26 CA CB C C sing 1.53 N N
27 CA C C C sing 1.51 N N
28 CA HA C H sing 1.09 N N
29 CB CAG C C sing 1.53 N N
30 CB CG1 C C sing 1.53 N N
31 CB CG2 C C sing 1.53 N N
32 CAG HAG C H sing 1.09 N N
33 CAG HAGA C H sing 1.09 N N
34 CAG HAGB C H sing 1.09 N N
35 CG1 HG1 C H sing 1.09 N N
36 CG1 HG1A C H sing 1.09 N N
37 CG1 HG1B C H sing 1.09 N N
38 CG2 HG2 C H sing 1.09 N N
39 CG2 HG2A C H sing 1.09 N N
40 CG2 HG2B C H sing 1.09 N N
41 C O C O doub 1.21 N N
42 CBI CBN C C sing 1.51 N N
43 CBI OAN C O doub 1.21 N N
44 NBC CBO N C sing 1.47 N N
45 NBC HNBC N H sing 0.97 N N
46 CBN OAO C O sing 1.43 N N
47 CBN HBN C H sing 1.09 N N
48 CBJ CBA C C sing 1.51 N N
49 CBA HBA C H sing 1.09 N N
50 CBA HBAA C H sing 1.09 N N
51 CAP CAR C C doub 1.38 N Y
52 CAP CAS C C sing 1.38 N Y
53 CAP HAP C H sing 1.08 N N
54 CBO CBN C C sing 1.53 N N
55 CBO CBA C C sing 1.53 N N
56 CBO HBO C H sing 1.09 N N
57 OAO HOAO O H sing 0.97 N N
58 CAV CBJ C C doub 1.38 N Y
59 CAV HAV C H sing 1.08 N N
60 CAW CBJ C C sing 1.38 N Y
61 CAW HAW C H sing 1.08 N N
62 CAR CAV C C sing 1.38 N Y
63 CAR HAR C H sing 1.08 N N
64 CAS CAW C C doub 1.38 N Y
65 CAS HAS C H sing 1.08 N N
66 CBH CBQ C C sing 1.51 N N
67 OAM CBH O C doub 1.21 N N
68 CBQ NBR C N sing 1.45 N N
69 CBQ HBQ C H sing 1.09 N N
70 CBU CBQ C C sing 1.55 N N
71 CBU CAI C C sing 1.53 N N
72 CAZ NBR C N sing 1.48 N N
73 CAZ HAZ C H sing 1.09 N N
74 CAZ HAZA C H sing 1.09 N N
75 CAH CBU C C sing 1.53 N N
76 CAH HAH C H sing 1.09 N N
77 CAH HAHA C H sing 1.09 N N
78 CAH HAHB C H sing 1.09 N N
79 CAI HAI C H sing 1.09 N N
80 CAI HAIA C H sing 1.09 N N
81 CAI HAIB C H sing 1.09 N N
82 SBE CBU S C sing 1.84 N N
83 SBE CAZ S C sing 1.84 N N
84 NBB CBL N C sing 1.47 N N
85 NBB HNBB N H sing 0.97 N N
86 CBL CBS C C sing 1.53 N N
87 CBL HBL C H sing 1.09 N N
88 CBL HBLA C H sing 1.09 N N
89 CBS CAB C C sing 1.53 N N
90 CBS CAC C C sing 1.53 N N
91 CBS CAD C C sing 1.53 N N
92 CAB HAB C H sing 1.09 N N
93 CAB HABA C H sing 1.09 N N
94 CAB HABB C H sing 1.09 N N
95 CAC HAC C H sing 1.09 N N
96 CAC HACA C H sing 1.09 N N
97 CAC HACB C H sing 1.09 N N
98 CAD HAD C H sing 1.09 N N
99 CAD HADA C H sing 1.09 N N
100 CAD HADB C H sing 1.09 N N
101 CB1 NAJ C N sing 1.35 N N
102 CBF N C N sing 1.35 N N
103 C NBC C N sing 1.35 N N
104 CBI NBR C N sing 1.35 N N
105 CBH NBB C N sing 1.35 N N



E13 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
E13 3lin Open in New Window Bound ligand 6 1