Chemical Components in the PDB

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SH0 : Summary

Code

SH0

One-letter code

X

Molecule name

3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,11S,12S,13S,16S,19S)-3,8,13,17-tetrakis(carboxylatomethyl)-8,13-dimethyl-1,2,3,4,7,8,11,12,13,16,19,20,22,24-tetradecahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoate

Systematic names

ProgramVersionName
ACDLabs 12.01 3,3',3'',3'''-[(1R,2S,3S,7S,8S,11S,12S,13S,19S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-1,2,3,7,8,11,12,13,19,20-decahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid
OpenEye OEToolkits 1.7.6 3-[(1R,2S,3S,5Z,7S,8S,9Z,12S,13S,14Z,19S)-3,8,13,17-tetrakis(2-hydroxy-2-oxoethyl)-7,12,18-tris(3-hydroxy-3-oxopropyl)-8,13-dimethyl-1,2,3,7,11,12,19,20,22,23-decahydroporphyrin-2-yl]propanoic acid

Formula

C42 H52 N4 O16

Formal charge

0

Molecular weight

868.879 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CCC1=C(C2=NC1CC5N=C(C=C4NC(=CC3NC(=C2)C(C)(C3CCC(=O)O)CC(=O)O)C(CC(=O)O)(C)C4CCC(=O)O)C(CC(=O)O)C5CCC(=O)O)CC(=O)O
SMILES CACTVS 3.385 C[C]1(CC(O)=O)[CH](CCC(O)=O)[CH]2NC1=CC3=N[CH](C[CH]4N=C(C=C5NC(=C2)[C](C)(CC(O)=O)[CH]5CCC(O)=O)[CH](CC(O)=O)[CH]4CCC(O)=O)C(=C3CC(O)=O)CCC(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC1(C(C2C=C3C(C(C(=CC4=NC(CC5C(=C(C(=N5)C=C1N2)CC(=O)O)CCC(=O)O)C(C4CC(=O)O)CCC(=O)O)N3)CCC(=O)O)(C)CC(=O)O)CCC(=O)O)CC(=O)O
Canonical SMILES CACTVS 3.385 C[C@]/1(CC(O)=O)[C@H](CCC(O)=O)[C@@H]\2NC/1=C/C3=N[C@@H](C[C@H]4N=C(/C=C/5NC(=C\2)\[C@@](C)(CC(O)=O)[C@@H]/5CCC(O)=O)[C@@H](CC(O)=O)[C@@H]4CCC(O)=O)C(=C3CC(O)=O)CCC(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@]\1([C@@H](C2/C=C\3/[C@@]([C@@H](/C(=C/C4=N[C@H](C[C@H]5C(=C(C(=N5)/C=C1\N2)CC(=O)O)CCC(=O)O)[C@H]([C@@H]4CC(=O)O)CCC(=O)O)/N3)CCC(=O)O)(C)CC(=O)O)CCC(=O)O)CC(=O)O

IUPAC InChI

InChI=1S/C42H52N4O16/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29/h14-16,19,21,23-26,30,45-46H,3-13,17-18H2,1-2H3,(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)/b29-14-,31-15-,32-16-/t19-,21-,23+,24+,25+,26-,30+,41-,42-/m0/s1

IUPAC InChI key

PTDGOSZHGZMQAZ-IIRIWOCESA-N
SH0

wwPDB Information

Atom count

114 (62 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-07-09

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



SH0 : Atoms of Molecule

Total Number of Atoms: 114
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 -0.455 2.933 0.197
2 C2 C C2 S N N 0 -1.566 3.927 -0.078
3 C3 C C3 S N N 0 -2.836 3.057 -0.229
4 C4 C C4 R N N 0 -2.409 1.786 0.54
5 C5 C C5 N N N 0 -2.937 0.534 -0.163
6 C6 C C6 N N N 0 -1.694 -2.524 0.325
7 C7 C C7 N N N 0 -3.132 -2.812 0.174
8 C8 C C8 N N N 0 -3.836 -1.72 0.448
9 C9 C C9 S N N 0 -2.835 -0.647 0.805
10 C10 C C10 N N N 0 -0.631 -3.506 0.116
11 C11 C C11 N N N 0 0.663 -3.155 0.143
12 C12 C C12 S N N 0 1.805 -4.132 -0.039
13 O12 O O12 N N N 0 -1.083 2.531 -2.283
14 C13 C C13 S N N 0 3.095 -3.329 0.197
15 O13 O O13 N N N 0 -6.346 4.578 1.43
16 C14 C C14 S N N 0 2.59 -1.931 0.621
17 C15 C C15 N N N 0 3.38 -0.876 -0.09
18 C16 C C16 N N N 0 3.02 0.375 -0.215
19 C17 C C17 S N N 0 3.908 1.44 -0.863
20 O17 O O17 N N N 0 -4.206 -5.355 -2.323
21 C18 C C18 S N N 0 3.356 2.735 -0.219
22 O18 O O18 N N N 0 -8.122 -1.82 2.898
23 C19 C C19 N N N 0 1.899 2.358 0.031
24 O1L O O1L N N N 0 1.939 -2.428 -2.067
25 O1M O O1M N N N 0 7.287 -3.356 2.844
26 O1Q O O1Q N N N 0 4.547 2.776 -4.301
27 O1R O O1R N N N 0 5.109 3.911 3.377
28 C20 C C20 N N N 0 0.91 3.257 0.09
29 N21 N N21 N N N 0 -0.94 1.782 0.529
30 N22 N N22 N N N 0 -1.513 -1.279 0.685
31 O22 O O22 N N N 0 -0.982 4.168 -3.765
32 N23 N N23 N N N 0 1.16 -1.889 0.315
33 O23 O O23 N N N 0 -7.707 2.999 0.695
34 N24 N N24 N N N 0 1.825 0.992 0.147
35 O27 O O27 N N N 0 -3.308 -3.338 -2.407
36 O28 O O28 N N N 0 -7.961 -1.41 0.733
37 C2A C C2A N N N 0 -1.287 4.694 -1.372
38 C2B C C2B N N N 0 -1.11 3.718 -2.506
39 O2L O O2L N N N 0 1.764 -3.827 -3.769
40 O2M O O2M N N N 0 5.634 -4.787 3.167
41 O2Q O O2Q N N N 0 5.156 3.324 -2.249
42 O2R O O2R N N N 0 4.035 5.831 3.594
43 C31 C C31 N N N 0 -4.044 3.724 0.433
44 C32 C C32 N N N 0 -5.3 2.896 0.154
45 C33 C C33 N N N 0 -6.489 3.553 0.807
46 C41 C C41 N N N 0 -5.335 -1.58 0.41
47 C42 C C42 N N N 0 -5.905 -1.804 1.813
48 C43 C C43 N N N 0 -7.404 -1.664 1.775
49 C51 C C51 N N N 0 3.924 -3.963 1.316
50 C52 C C52 N N N 0 5.256 -3.222 1.446
51 C53 C C53 N N N 0 6.072 -3.846 2.549
52 C61 C C61 N N N 0 4.075 3.043 1.096
53 C62 C C62 N N N 0 3.593 4.39 1.638
54 C63 C C63 N N N 0 4.301 4.693 2.933
55 C7A C C7A N N N 0 -3.714 -4.142 -0.23
56 C7B C C7B N N N 0 -3.727 -4.248 -1.733
57 C81 C C81 N N N 0 1.79 -4.7 -1.459
58 C82 C C82 N N N 0 1.837 -3.569 -2.454
59 C86 C C86 N N N 0 3.722 1.459 -2.382
60 C87 C C87 N N N 0 4.528 2.588 -2.972
61 CMA C CMA N N N 0 1.695 -5.266 0.982
62 CMB C CMB N N N 0 5.378 1.227 -0.494
63 H2 H H2 N N N 0 -1.675 4.616 0.759
64 H3 H H3 N N N 0 -3.037 2.834 -1.277
65 H4 H H4 N N N 0 -2.778 1.834 1.56
66 H5 H H5 N N N 0 -3.978 0.685 -0.447
67 H5A H H5A N N N 0 -2.338 0.333 -1.051
68 H9 H H9 N N N 0 -2.996 -0.308 1.829
69 H10 H H10 N N N 0 -0.896 -4.546 -0.045
70 H13 H H13 N N N 0 3.678 -3.263 -0.721
71 H14 H H14 N N N 0 2.731 -1.828 1.704
72 H15 H H15 N N N 0 4.335 -1.166 -0.548
73 H18 H H18 N N N 0 3.429 3.576 -0.909
74 H20 H H20 N N N 0 1.18 4.315 0.076
75 HN23 H HN23 N N N 0 0.636 -1.076 0.242
76 HN24 H HN24 N N N 0 1.036 0.514 0.447
77 H2A H H2A N N N 0 -2.126 5.356 -1.589
78 H2AA H H2AA N N N 0 -0.379 5.285 -1.255
79 H31 H H31 N N N 0 -3.88 3.785 1.509
80 H31A H H31A N N N 0 -4.172 4.727 0.027
81 H32 H H32 N N N 0 -5.463 2.835 -0.922
82 H32A H H32A N N N 0 -5.171 1.893 0.56
83 H41 H H41 N N N 0 -5.598 -0.579 0.068
84 H41A H H41A N N N 0 -5.753 -2.319 -0.274
85 H42 H H42 N N N 0 -5.642 -2.805 2.155
86 H42A H H42A N N N 0 -5.487 -1.065 2.497
87 H51 H H51 N N N 0 3.377 -3.895 2.257
88 H51A H H51A N N N 0 4.112 -5.01 1.081
89 H52 H H52 N N N 0 5.803 -3.29 0.506
90 H52A H H52A N N N 0 5.067 -2.174 1.682
91 H61 H H61 N N N 0 3.856 2.26 1.822
92 H61A H H61A N N N 0 5.15 3.086 0.921
93 H62 H H62 N N N 0 3.812 5.173 0.912
94 H62A H H62A N N N 0 2.518 4.347 1.813
95 H7A H H7A N N N 0 -3.106 -4.945 0.186
96 H7AA H H7AA N N N 0 -4.733 -4.223 0.149
97 H81 H H81 N N N 0 2.658 -5.344 -1.602
98 H81A H H81A N N N 0 0.879 -5.279 -1.61
99 H86 H H86 N N N 0 4.061 0.512 -2.802
100 H86A H H86A N N N 0 2.668 1.604 -2.616
101 HMA H HMA N N N 0 0.762 -5.807 0.826
102 HMAA H HMAA N N N 0 2.536 -5.948 0.859
103 HMAB H HMAB N N N 0 1.71 -4.85 1.99
104 HMB H HMB N N N 0 5.708 0.255 -0.863
105 HMBA H HMBA N N N 0 5.984 2.012 -0.947
106 HMBB H HMBB N N N 0 5.489 1.261 0.59
107 H17B H H17B N N N 0 -4.194 -5.377 -3.29
108 H18B H H18B N N N 0 -9.081 -1.721 2.824
109 H19B H H19B N N N 0 7.773 -3.789 3.559
110 H20B H H20B N N N 0 5.077 3.512 -4.633
111 H21B H H21B N N N 0 -0.871 3.504 -4.459
112 H22B H H22B N N N 0 -8.439 3.457 1.13
113 H23B H H23B N N N 0 1.797 -3.069 -4.368
114 H24B H H24B N N N 0 4.514 5.981 4.42



SH0 : Chemical Bonds

Total Number of Bonds: 118
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.52 N N
2 C1 C20 C C sing 1.41 N N
3 C1 N21 C N doub 1.29 N N
4 C2 C3 C C sing 1.55 N N
5 C2 C2A C C sing 1.53 N N
6 C3 C4 C C sing 1.55 N N
7 C3 C31 C C sing 1.53 N N
8 C4 C5 C C sing 1.53 N N
9 C4 N21 C N sing 1.47 N N
10 C5 C9 C C sing 1.53 N N
11 C6 C7 C C sing 1.47 N N
12 C6 C10 C C sing 1.46 N N
13 C6 N22 C N doub 1.31 N N
14 C7 C8 C C doub 1.33 N N
15 C7 C7A C C sing 1.51 N N
16 C8 C9 C C sing 1.51 N N
17 C8 C41 C C sing 1.51 N N
18 C9 N22 C N sing 1.47 N N
19 C10 C11 C C doub 1.34 Z N
20 C11 C12 C C sing 1.51 N N
21 C11 N23 C N sing 1.37 N N
22 C12 C13 C C sing 1.54 N N
23 C12 C81 C C sing 1.53 N N
24 C12 CMA C C sing 1.53 N N
25 O12 C2B O C doub 1.21 N N
26 C13 C14 C C sing 1.55 N N
27 C13 C51 C C sing 1.53 N N
28 O13 C33 O C doub 1.21 N N
29 C14 C15 C C sing 1.5 N N
30 C14 N23 C N sing 1.46 N N
31 C15 C16 C C doub 1.31 Z N
32 C16 C17 C C sing 1.53 N N
33 C16 N24 C N sing 1.39 N N
34 C17 C18 C C sing 1.55 N N
35 C17 C86 C C sing 1.53 N N
36 C17 CMB C C sing 1.53 N N
37 O17 C7B O C sing 1.34 N N
38 C18 C19 C C sing 1.53 N N
39 C18 C61 C C sing 1.53 N N
40 O18 C43 O C sing 1.34 N N
41 C19 C20 C C doub 1.34 Z N
42 C19 N24 C N sing 1.37 N N
43 O1L C82 O C doub 1.21 N N
44 O1M C53 O C sing 1.34 N N
45 O1Q C87 O C sing 1.34 N N
46 O1R C63 O C doub 1.21 N N
47 O22 C2B O C sing 1.34 N N
48 O23 C33 O C sing 1.34 N N
49 O27 C7B O C doub 1.21 N N
50 O28 C43 O C doub 1.21 N N
51 C2A C2B C C sing 1.51 N N
52 O2L C82 O C sing 1.34 N N
53 O2M C53 O C doub 1.21 N N
54 O2Q C87 O C doub 1.21 N N
55 O2R C63 O C sing 1.34 N N
56 C31 C32 C C sing 1.53 N N
57 C32 C33 C C sing 1.51 N N
58 C41 C42 C C sing 1.53 N N
59 C42 C43 C C sing 1.51 N N
60 C51 C52 C C sing 1.53 N N
61 C52 C53 C C sing 1.51 N N
62 C61 C62 C C sing 1.53 N N
63 C62 C63 C C sing 1.51 N N
64 C7A C7B C C sing 1.51 N N
65 C81 C82 C C sing 1.51 N N
66 C86 C87 C C sing 1.51 N N
67 C2 H2 C H sing 1.09 N N
68 C3 H3 C H sing 1.09 N N
69 C4 H4 C H sing 1.09 N N
70 C5 H5 C H sing 1.09 N N
71 C5 H5A C H sing 1.09 N N
72 C9 H9 C H sing 1.09 N N
73 C10 H10 C H sing 1.09 N N
74 C13 H13 C H sing 1.09 N N
75 C14 H14 C H sing 1.1 N N
76 C15 H15 C H sing 1.1 N N
77 C18 H18 C H sing 1.09 N N
78 C20 H20 C H sing 1.09 N N
79 N23 HN23 N H sing 0.97 N N
80 N24 HN24 N H sing 0.97 N N
81 C2A H2A C H sing 1.09 N N
82 C2A H2AA C H sing 1.09 N N
83 C31 H31 C H sing 1.09 N N
84 C31 H31A C H sing 1.09 N N
85 C32 H32 C H sing 1.09 N N
86 C32 H32A C H sing 1.09 N N
87 C41 H41 C H sing 1.09 N N
88 C41 H41A C H sing 1.09 N N
89 C42 H42 C H sing 1.09 N N
90 C42 H42A C H sing 1.09 N N
91 C51 H51 C H sing 1.09 N N
92 C51 H51A C H sing 1.09 N N
93 C52 H52 C H sing 1.09 N N
94 C52 H52A C H sing 1.09 N N
95 C61 H61 C H sing 1.09 N N
96 C61 H61A C H sing 1.09 N N
97 C62 H62 C H sing 1.09 N N
98 C62 H62A C H sing 1.09 N N
99 C7A H7A C H sing 1.09 N N
100 C7A H7AA C H sing 1.09 N N
101 C81 H81 C H sing 1.09 N N
102 C81 H81A C H sing 1.09 N N
103 C86 H86 C H sing 1.09 N N
104 C86 H86A C H sing 1.09 N N
105 CMA HMA C H sing 1.09 N N
106 CMA HMAA C H sing 1.09 N N
107 CMA HMAB C H sing 1.09 N N
108 CMB HMB C H sing 1.09 N N
109 CMB HMBA C H sing 1.09 N N
110 CMB HMBB C H sing 1.09 N N
111 O17 H17B O H sing 0.97 N N
112 O18 H18B O H sing 0.97 N N
113 O1M H19B O H sing 0.97 N N
114 O1Q H20B O H sing 0.97 N N
115 O22 H21B O H sing 0.97 N N
116 O23 H22B O H sing 0.97 N N
117 O2L H23B O H sing 0.97 N N
118 O2R H24B O H sing 0.97 N N



SH0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SH0 2v4j Open in New Window Bound ligand 2 1