Chemical Components in the PDB

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1HA : Summary

Code

1HA

One-letter code

X

Molecule name

1-hydroxy-2-naphthoyl-CoA

Systematic names

ProgramVersionName
ACDLabs 12.01 S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 1-hydroxynaphthalene-2-carbothioate (non-preferred name)
OpenEye OEToolkits 1.7.6 S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 1-oxidanylnaphthalene-2-carbothioate

Formula

C32 H42 N7 O18 P3 S

Formal charge

0

Molecular weight

937.698 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)c5ccc4ccccc4c5O
SMILES CACTVS 3.370 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O
SMILES OpenEye OEToolkits 1.7.6 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O)O
Canonical SMILES CACTVS 3.370 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O)O

IUPAC InChI

InChI=1S/C32H42N7O18P3S/c1-32(2,26(43)29(44)35-10-9-21(40)34-11-12-61-31(45)19-8-7-17-5-3-4-6-18(17)23(19)41)14-54-60(51,52)57-59(49,50)53-13-20-25(56-58(46,47)48)24(42)30(55-20)39-16-38-22-27(33)36-15-37-28(22)39/h3-8,15-16,20,24-26,30,41-43H,9-14H2,1-2H3,(H,34,40)(H,35,44)(H,49,50)(H,51,52)(H2,33,36,37)(H2,46,47,48)/t20-,24-,25-,26+,30-/m1/s1

IUPAC InChI key

ZHSLHXZSNOSMQG-HSJNEKGZSA-N
1HA

wwPDB Information

Atom count

103 (61 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-11-29

Last modified at

2013-05-03

Status

Released

Obsoleted

Not Assigned



1HA : 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 OAJ O OAJ N N N 0 -14.19 1.237 2.487
2 CBT C CBT N Y N 0 -14.521 1.688 1.253
3 CBW C CBW N Y N 0 -15.722 2.399 1.053
4 CAV C CAV N Y N 0 -16.598 2.658 2.12
5 CAR C CAR N Y N 0 -17.751 3.348 1.894
6 CAQ C CAQ N Y N 0 -18.074 3.803 0.618
7 CAU C CAU N Y N 0 -17.247 3.57 -0.439
8 CBV C CBV N Y N 0 -16.051 2.862 -0.245
9 CAW C CAW N Y N 0 -15.176 2.607 -1.319
10 CAT C CAT N Y N 0 -14.024 1.921 -1.113
11 CBU C CBU N Y N 0 -13.677 1.458 0.17
12 CBR C CBR N N N 0 -12.417 0.722 0.366
13 OAF O OAF N N N 0 -12.116 0.316 1.473
14 SBO S SBO N N N 0 -11.345 0.428 -1.001
15 CBA C CBA N N N 0 -10.019 -0.482 -0.171
16 CAY C CAY N N N 0 -8.94 -0.854 -1.191
17 NBH N NBH N N N 0 -7.867 -1.591 -0.519
18 CBP C CBP N N N 0 -6.803 -2.024 -1.224
19 OAD O OAD N N N 0 -6.734 -1.803 -2.415
20 CBB C CBB N N N 0 -5.699 -2.782 -0.534
21 CAZ C CAZ N N N 0 -4.621 -3.154 -1.553
22 NBI N NBI N N N 0 -3.547 -3.891 -0.881
23 CBQ C CBQ N N N 0 -2.483 -4.324 -1.587
24 OAE O OAE N N N 0 -2.457 -4.186 -2.791
25 CBZ C CBZ R N N 0 -1.326 -4.979 -0.878
26 OAK O OAK N N N 0 -1.697 -5.274 0.47
27 CCF C CCF N N N 0 -0.124 -4.032 -0.881
28 CAA C CAA N N N 0 0.367 -3.835 -2.316
29 CAB C CAB N N N 0 -0.538 -2.682 -0.293
30 CBD C CBD N N N 0 1.001 -4.634 -0.036
31 OBK O OBK N N N 0 2.123 -3.749 -0.038
32 PCI P PCI N N N 0 3.49 -4.065 0.752
33 OAP O OAP N N N 0 4.196 -5.36 0.107
34 OAI O OAI N N N 0 3.187 -4.327 2.177
35 OBN O OBN N N N 0 4.48 -2.801 0.638
36 PCH P PCH N N N 0 5.814 -2.351 1.419
37 OAO O OAO N N N 0 6.718 -3.513 1.562
38 OAH O OAH N N N 0 5.42 -1.795 2.878
39 O5' O O5' N N N 0 6.558 -1.191 0.587
40 C5' C C5' N N N 0 7.827 -0.653 0.965
41 C4' C C4' R N N 0 8.243 0.425 -0.038
42 O4' O O4' N N N 0 7.398 1.589 0.095
43 C3' C C3' S N N 0 9.667 0.933 0.28
44 O3' O O3' N N N 0 10.627 0.292 -0.562
45 PCG P PCG N N N 0 11.838 -0.602 0.011
46 OAM O OAM N N N 0 12.622 0.194 0.982
47 OAN O OAN N N N 0 11.242 -1.906 0.744
48 OAG O OAG N N N 0 12.791 -1.057 -1.204
49 C2' C C2' R N N 0 9.603 2.446 -0.028
50 O2' O O2' N N N 0 10.521 2.785 -1.069
51 C1' C C1' R N N 0 8.148 2.673 -0.495
52 N9 N N9 N Y N 0 7.651 3.962 -0.007
53 C8 C C8 N Y N 0 6.982 4.178 1.162
54 N7 N N7 N Y N 0 6.69 5.441 1.279
55 C5 C C5 N Y N 0 7.15 6.113 0.196
56 C4 C C4 N Y N 0 7.777 5.173 -0.639
57 N3 N N3 N Y N 0 8.323 5.584 -1.778
58 C2 C C2 N Y N 0 8.282 6.854 -2.122
59 N1 N N1 N Y N 0 7.707 7.774 -1.37
60 C6 C C6 N Y N 0 7.128 7.456 -0.217
61 N6 N N6 N N N 0 6.529 8.427 0.567
62 H1 H H1 N N N 0 -14.516 0.348 2.682
63 H2 H H2 N N N 0 -16.36 2.31 3.114
64 H3 H H3 N N N 0 -18.423 3.545 2.716
65 H7 H H7 N N N 0 -13.362 1.731 -1.945
66 H4 H H4 N N N 0 -18.994 4.348 0.465
67 H5 H H5 N N N 0 -17.512 3.929 -1.423
68 H6 H H6 N N N 0 -15.424 2.958 -2.31
69 H8 H H8 N N N 0 -9.582 0.142 0.608
70 H9 H H9 N N N 0 -10.425 -1.389 0.276
71 H10 H H10 N N N 0 -9.377 -1.479 -1.97
72 H11 H H11 N N N 0 -8.534 0.053 -1.637
73 H12 H H12 N N N 0 -7.922 -1.768 0.433
74 H18 H H18 N N N 0 -1.061 -5.903 -1.393
75 H13 H H13 N N N 0 -5.262 -2.158 0.246
76 H14 H H14 N N N 0 -6.105 -3.689 -0.087
77 H15 H H15 N N N 0 -5.057 -3.779 -2.332
78 H16 H H16 N N N 0 -4.214 -2.247 -2.0
79 H17 H H17 N N N 0 -3.602 -4.068 0.071
80 H19 H H19 N N N 0 -1.946 -4.496 0.988
81 H20 H H20 N N N 0 -0.407 -3.335 -2.899
82 H21 H H21 N N N 0 1.269 -3.223 -2.311
83 H22 H H22 N N N 0 0.588 -4.805 -2.762
84 H23 H H23 N N N 0 -0.887 -2.823 0.73
85 H24 H H24 N N N 0 0.319 -2.007 -0.294
86 H25 H H25 N N N 0 -1.339 -2.253 -0.895
87 H26 H H26 N N N 0 0.651 -4.775 0.987
88 H27 H H27 N N N 0 1.296 -5.596 -0.455
89 H28 H H28 N N N 0 4.424 -5.259 -0.827
90 H29 H H29 N N N 0 4.827 -1.031 2.861
91 H30 H H30 N N N 0 7.753 -0.214 1.96
92 H31 H H31 N N N 0 8.572 -1.449 0.973
93 H32 H H32 N N N 0 8.198 0.035 -1.054
94 H33 H H33 N N N 0 9.908 0.765 1.329
95 H39 H H39 N N N 0 6.733 3.415 1.883
96 H34 H H34 N N N 0 10.716 -2.476 0.166
97 H35 H H35 N N N 0 13.543 -1.6 -0.932
98 H36 H H36 N N N 0 9.811 3.028 0.87
99 H37 H H37 N N N 0 10.522 3.723 -1.303
100 H38 H H38 N N N 0 8.087 2.629 -1.582
101 H40 H H40 N N N 0 8.736 7.155 -3.055
102 H41 H H41 N N N 0 6.119 8.185 1.411
103 H42 H H42 N N N 0 6.52 9.351 0.271



1HA : Chemical Bonds

Total Number of Bonds: 107
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAI PCI O P doub 1.48 N N
2 OAP PCI O P sing 1.61 N N
3 PCI OBN P O sing 1.61 N N
4 PCI OBK P O sing 1.61 N N
5 OAO PCH O P doub 1.48 N N
6 OBN PCH O P sing 1.61 N N
7 OBK CBD O C sing 1.43 N N
8 PCH OAH P O sing 1.61 N N
9 PCH O5' P O sing 1.61 N N
10 CBD CCF C C sing 1.53 N N
11 CAB CCF C C sing 1.53 N N
12 C5' O5' C O sing 1.43 N N
13 C5' C4' C C sing 1.53 N N
14 OAM PCG O P doub 1.48 N N
15 CCF CBZ C C sing 1.53 N N
16 CCF CAA C C sing 1.53 N N
17 C4' C3' C C sing 1.54 N N
18 C4' O4' C O sing 1.44 N N
19 CBZ OAK C O sing 1.43 N N
20 CBZ CBQ C C sing 1.51 N N
21 C3' O3' C O sing 1.43 N N
22 C3' C2' C C sing 1.55 N N
23 PCG OAN P O sing 1.61 N N
24 PCG O3' P O sing 1.61 N N
25 PCG OAG P O sing 1.61 N N
26 O4' C1' O C sing 1.44 N N
27 OAE CBQ O C doub 1.21 N N
28 CBQ NBI C N sing 1.35 N N
29 C2' C1' C C sing 1.54 N N
30 C2' O2' C O sing 1.43 N N
31 C1' N9 C N sing 1.47 N N
32 C8 N9 C N sing 1.36 N Y
33 C8 N7 C N doub 1.3 N Y
34 NBI CAZ N C sing 1.47 N N
35 N9 C4 N C sing 1.37 N Y
36 N7 C5 N C sing 1.36 N Y
37 CAZ CBB C C sing 1.53 N N
38 C4 C5 C C doub 1.4 N Y
39 C4 N3 C N sing 1.33 N Y
40 CBB CBP C C sing 1.51 N N
41 C5 C6 C C sing 1.41 N Y
42 N3 C2 N C doub 1.32 N Y
43 CBP OAD C O doub 1.21 N N
44 CBP NBH C N sing 1.35 N N
45 C6 N6 C N sing 1.38 N N
46 C6 N1 C N doub 1.33 N Y
47 C2 N1 C N sing 1.32 N Y
48 NBH CAY N C sing 1.46 N N
49 CAY CBA C C sing 1.53 N N
50 CBA SBO C S sing 1.81 N N
51 OAF CBR O C doub 1.22 N N
52 SBO CBR S C sing 1.76 N N
53 CBR CBU C C sing 1.47 N N
54 CBU CBT C C doub 1.39 N Y
55 CBU CAT C C sing 1.41 N Y
56 OAJ CBT O C sing 1.35 N N
57 CBT CBW C C sing 1.41 N Y
58 CAT CAW C C doub 1.36 N Y
59 CAW CBV C C sing 1.41 N Y
60 CBW CBV C C doub 1.42 N Y
61 CBW CAV C C sing 1.4 N Y
62 CBV CAU C C sing 1.4 N Y
63 CAV CAR C C doub 1.36 N Y
64 CAU CAQ C C doub 1.36 N Y
65 CAR CAQ C C sing 1.39 N Y
66 OAJ H1 O H sing 0.97 N N
67 CAV H2 C H sing 1.08 N N
68 CAR H3 C H sing 1.08 N N
69 CAQ H4 C H sing 1.08 N N
70 CAU H5 C H sing 1.08 N N
71 CAW H6 C H sing 1.08 N N
72 CAT H7 C H sing 1.08 N N
73 CBA H8 C H sing 1.09 N N
74 CBA H9 C H sing 1.09 N N
75 CAY H10 C H sing 1.09 N N
76 CAY H11 C H sing 1.09 N N
77 NBH H12 N H sing 0.97 N N
78 CBB H13 C H sing 1.09 N N
79 CBB H14 C H sing 1.09 N N
80 CAZ H15 C H sing 1.09 N N
81 CAZ H16 C H sing 1.09 N N
82 NBI H17 N H sing 0.97 N N
83 CBZ H18 C H sing 1.09 N N
84 OAK H19 O H sing 0.97 N N
85 CAA H20 C H sing 1.09 N N
86 CAA H21 C H sing 1.09 N N
87 CAA H22 C H sing 1.09 N N
88 CAB H23 C H sing 1.09 N N
89 CAB H24 C H sing 1.09 N N
90 CAB H25 C H sing 1.09 N N
91 CBD H26 C H sing 1.09 N N
92 CBD H27 C H sing 1.09 N N
93 OAP H28 O H sing 0.97 N N
94 OAH H29 O H sing 0.97 N N
95 C5' H30 C H sing 1.09 N N
96 C5' H31 C H sing 1.09 N N
97 C4' H32 C H sing 1.09 N N
98 C3' H33 C H sing 1.09 N N
99 OAN H34 O H sing 0.97 N N
100 OAG H35 O H sing 0.97 N N
101 C2' H36 C H sing 1.09 N N
102 O2' H37 O H sing 0.97 N N
103 C1' H38 C H sing 1.09 N N
104 C8 H39 C H sing 1.08 N N
105 C2 H40 C H sing 1.08 N N
106 N6 H41 N H sing 0.97 N N
107 N6 H42 N H sing 0.97 N N



1HA : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
1HA 4i42 Open in New Window Bound ligand 11 1
1HA 4i52 Open in New Window Bound ligand 9 1
1HA 4qij Open in New Window Bound ligand 12 1