Chemical Components in the PDB

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H01 : Summary

Code

H01

One-letter code

X

Molecule name

PROTOPORPHYRIN IX 2,4-DISULFONIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 3,3'-(3,7,12,17-tetramethyl-8,13-disulfo-22,24-dihydroporphyrin-2,18-diyl)dipropanoic acid

Formula

C30 H32 N4 O10 S2

Formal charge

0

Molecular weight

672.726 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=S(=O)(O)C5=C(C=2NC5=Cc1c(c(c(n1)C=C4NC(=Cc3c(c(c(C=2)n3)S(=O)(=O)O)C)C(=C4CCC(=O)O)C)CCC(=O)O)C)C
SMILES CACTVS 3.341 CC1=C(CCC(O)=O)C2=Cc3[nH]c(C=C4NC(=Cc5[nH]c(C=C1N2)c(C)c5[S](O)(=O)=O)C(=C4[S](O)(=O)=O)C)c(C)c3CCC(O)=O
SMILES OpenEye OEToolkits 1.5.0 Cc1c2[nH]c(c1CCC(=O)O)C=C3C(=C(C(=Cc4c(c(c([nH]4)C=C5C(=C(C(=C2)N5)S(=O)(=O)O)C)S(=O)(=O)O)C)N3)C)CCC(=O)O
Canonical SMILES CACTVS 3.341 CC/1=C(CCC(O)=O)\C2=C\c3[nH]c(\C=C4/N\C(=C/c5[nH]c(\C=C/1N2)c(C)c5[S](O)(=O)=O)C(=C4[S](O)(=O)=O)C)c(C)c3CCC(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c\2[nH]c(c1CCC(=O)O)\C=C/3\C(=C(/C(=C/c4c(c(c([nH]4)C=C5C(=C(/C(=C2)/N5)S(=O)(=O)O)C)S(=O)(=O)O)C)/N3)C)CCC(=O)O

IUPAC InChI

InChI=1S/C30H32N4O10S2/c1-13-17(5-7-27(35)36)23-12-24-18(6-8-28(37)38)14(2)20(32-24)10-25-30(46(42,43)44)16(4)22(34-25)11-26-29(45(39,40)41)15(3)21(33-26)9-19(13)31-23/h9-12,31-34H,5-8H2,1-4H3,(H,35,36)(H,37,38)(H,39,40,41)(H,42,43,44)/b19-9-,20-10-,21-9-,22-11-,23-12-,24-12-,25-10-,26-11-

IUPAC InChI key

VFNOXNYLBHFZNR-IZAUZZAISA-N
H01

wwPDB Information

Atom count

78 (46 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-06-11

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



H01 : Atoms of Molecule

Total Number of Atoms: 78
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 1.877 -1.141 -0.007
2 C11 C C11 N N N 0 1.678 -2.515 -0.006
3 C12 C C12 N N N 0 2.939 -3.135 -0.218
4 O1 O O1 N N N 0 2.194 -5.401 -1.14
5 O2 O O2 N N N 0 4.611 -5.027 -0.622
6 C13 C C13 N N N 0 3.875 -2.17 -0.322
7 C15 C C15 N N N 0 3.881 0.289 -0.196
8 C14 C C14 N N N 0 3.237 -0.909 -0.176
9 C16 C C16 N N N 0 3.031 5.25 0.293
10 O3 O O3 N N N 0 3.021 -5.448 1.067
11 O4 O O4 N N N 0 5.936 3.284 -1.447
12 C21 C C21 N Y N 0 3.177 1.559 -0.044
13 C22 C C22 N Y N 0 3.805 2.792 0.045
14 C23 C C23 N Y N 0 2.811 3.764 0.168
15 C24 C C24 N Y N 0 1.586 3.116 0.153
16 C25 C C25 N N N 0 0.297 3.796 0.236
17 C26 C C26 N N N 0 5.347 -2.391 -0.554
18 O41 O O41 N N N 0 -7.204 3.307 0.25
19 O42 O O42 N N N 0 -7.42 3.072 -1.937
20 C49 C C49 N N N 0 -6.678 3.105 -0.819
21 C48 C C48 N N N 0 -5.188 2.89 -0.897
22 C47 C C47 N N N 0 -4.586 2.977 0.507
23 C33 C C33 N N N 0 -3.096 2.762 0.429
24 C32 C C32 N N N 0 -2.162 3.732 0.353
25 C34 C C34 N N N 0 -2.437 1.503 0.424
26 C46 C C46 N N N 0 -2.431 5.215 0.333
27 C31 C C31 N N N 0 -0.883 3.119 0.294
28 N3 N N3 N N N 0 -1.073 1.742 0.315
29 C35 C C35 N N N 0 -3.077 0.307 0.523
30 C41 C C41 N Y N 0 -2.368 -0.97 0.506
31 N4 N N4 N Y N 0 -1.023 -1.175 0.315
32 C42 C C42 N Y N 0 -2.969 -2.205 0.684
33 C37 C C37 N N N 0 -4.434 -2.454 0.937
34 C38 C C38 N N N 0 -5.16 -2.629 -0.398
35 C39 C C39 N N N 0 -6.624 -2.878 -0.144
36 O32 O O32 N N N 0 -7.463 -3.063 -1.176
37 O31 O O31 N N N 0 -7.044 -2.912 0.988
38 C43 C C43 N Y N 0 -1.972 -3.178 0.585
39 C36 C C36 N N N 0 -2.166 -4.667 0.714
40 C44 C C44 N Y N 0 -0.772 -2.527 0.347
41 C45 C C45 N N N 0 0.509 -3.196 0.159
42 S1 S S1 N N N 0 3.23 -4.87 -0.325
43 N2 N N2 N Y N 0 1.821 1.766 0.044
44 S2 S S2 N N N 0 5.543 3.08 0.009
45 O5 O O5 N N N 0 6.158 1.868 0.425
46 O6 O O6 N N N 0 5.757 4.324 0.661
47 HN1 H HN1 N N N 0 1.189 -0.463 0.089
48 H15 H H15 N N N 0 4.959 0.308 -0.331
49 H161 H 1H16 N N N 0 3.047 5.7 -0.7
50 H162 H 2H16 N N N 0 2.222 5.689 0.878
51 H163 H 3H16 N N N 0 3.982 5.436 0.792
52 HO3 H HO3 N N N 0 3.158 -6.404 1.12
53 HO4 H HO4 N N N 0 6.879 3.451 -1.58
54 H25 H H25 N N N 0 0.282 4.883 0.252
55 H261 H 1H26 N N N 0 5.548 -2.405 -1.626
56 H262 H 2H26 N N N 0 5.913 -1.585 -0.089
57 H263 H 3H26 N N N 0 5.644 -3.344 -0.116
58 HO42 H HO42 N N N 0 -8.371 3.215 -1.836
59 H481 H 1H48 N N N 0 -4.985 1.906 -1.319
60 H482 H 2H48 N N N 0 -4.743 3.657 -1.531
61 H471 H 1H47 N N N 0 -4.79 3.961 0.929
62 H472 H 2H47 N N N 0 -5.031 2.211 1.141
63 H461 H 1H46 N N N 0 -2.437 5.597 1.354
64 H462 H 2H46 N N N 0 -1.651 5.718 -0.238
65 H463 H 3H46 N N N 0 -3.399 5.403 -0.131
66 HN3 H HN3 N N N 0 -0.377 1.067 0.264
67 H35 H H35 N N N 0 -4.16 0.309 0.618
68 HN4 H HN4 N N N 0 -0.359 -0.481 0.179
69 H371 H 1H37 N N N 0 -4.55 -3.357 1.536
70 H372 H 2H37 N N N 0 -4.859 -1.605 1.474
71 H381 H 1H38 N N N 0 -5.043 -1.726 -0.996
72 H382 H 2H38 N N N 0 -4.735 -3.478 -0.934
73 HO32 H HO32 N N N 0 -8.393 -3.219 -0.964
74 H361 H 1H36 N N N 0 -2.378 -5.092 -0.267
75 H362 H 2H36 N N N 0 -1.259 -5.117 1.118
76 H363 H 3H36 N N N 0 -3.001 -4.867 1.385
77 H45 H H45 N N N 0 0.542 -4.283 0.15
78 HN2 H HN2 N N N 0 1.142 1.074 0.031



H01 : Chemical Bonds

Total Number of Bonds: 82
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C11 N C sing 1.39 N N
2 N1 C14 N C sing 1.39 N N
3 N1 HN1 N H sing 0.97 N N
4 C11 C45 C C doub 1.36 Z N
5 C11 C12 C C sing 1.42 N N
6 C12 S1 C S sing 1.76 N N
7 C12 C13 C C doub 1.35 N N
8 O1 S1 O S doub 1.42 N N
9 O2 S1 O S doub 1.42 N N
10 C13 C14 C C sing 1.42 N N
11 C13 C26 C C sing 1.51 N N
12 C15 C21 C C sing 1.46 N N
13 C15 C14 C C doub 1.36 Z N
14 C15 H15 C H sing 1.09 N N
15 C16 C23 C C sing 1.51 N N
16 C16 H161 C H sing 1.09 N N
17 C16 H162 C H sing 1.09 N N
18 C16 H163 C H sing 1.09 N N
19 O3 S1 O S sing 1.52 N N
20 O3 HO3 O H sing 0.97 N N
21 O4 S2 O S sing 1.52 N N
22 O4 HO4 O H sing 0.97 N N
23 C21 N2 C N sing 1.37 N Y
24 C21 C22 C C doub 1.39 N Y
25 C22 C23 C C sing 1.4 N Y
26 C22 S2 C S sing 1.76 N N
27 C23 C24 C C doub 1.39 N Y
28 C24 C25 C C sing 1.46 N N
29 C24 N2 C N sing 1.37 N Y
30 C25 C31 C C doub 1.36 Z N
31 C25 H25 C H sing 1.09 N N
32 C26 H261 C H sing 1.09 N N
33 C26 H262 C H sing 1.09 N N
34 C26 H263 C H sing 1.09 N N
35 O41 C49 O C doub 1.21 N N
36 C49 O42 C O sing 1.34 N N
37 C49 C48 C C sing 1.51 N N
38 O42 HO42 O H sing 0.97 N N
39 C48 C47 C C sing 1.53 N N
40 C48 H481 C H sing 1.09 N N
41 C48 H482 C H sing 1.09 N N
42 C47 C33 C C sing 1.51 N N
43 C47 H471 C H sing 1.09 N N
44 C47 H472 C H sing 1.09 N N
45 C33 C32 C C doub 1.35 N N
46 C33 C34 C C sing 1.42 N N
47 C32 C46 C C sing 1.51 N N
48 C32 C31 C C sing 1.42 N N
49 C46 H461 C H sing 1.09 N N
50 C46 H462 C H sing 1.09 N N
51 C46 H463 C H sing 1.09 N N
52 C31 N3 C N sing 1.39 N N
53 N3 C34 N C sing 1.39 N N
54 N3 HN3 N H sing 0.97 N N
55 C34 C35 C C doub 1.36 Z N
56 C35 C41 C C sing 1.46 N N
57 C35 H35 C H sing 1.09 N N
58 C41 C42 C C doub 1.38 N Y
59 C41 N4 C N sing 1.37 N Y
60 N4 C44 N C sing 1.38 N Y
61 N4 HN4 N H sing 0.97 N N
62 C42 C37 C C sing 1.51 N N
63 C42 C43 C C sing 1.4 N Y
64 C37 C38 C C sing 1.53 N N
65 C37 H371 C H sing 1.09 N N
66 C37 H372 C H sing 1.09 N N
67 C38 C39 C C sing 1.51 N N
68 C38 H381 C H sing 1.09 N N
69 C38 H382 C H sing 1.09 N N
70 C39 O31 C O doub 1.21 N N
71 C39 O32 C O sing 1.34 N N
72 O32 HO32 O H sing 0.97 N N
73 C43 C36 C C sing 1.51 N N
74 C43 C44 C C doub 1.39 N Y
75 C36 H361 C H sing 1.09 N N
76 C36 H362 C H sing 1.09 N N
77 C36 H363 C H sing 1.09 N N
78 C44 C45 C C sing 1.46 N N
79 C45 H45 C H sing 1.09 N N
80 N2 HN2 N H sing 0.97 N N
81 S2 O6 S O doub 1.42 N N
82 S2 O5 S O doub 1.42 N N



H01 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
H01 2q2n Open in New Window Bound ligand 1 1
H01 2q2o Open in New Window Bound ligand 1 1