Receptor
PDB id Resolution Class Description Source Keywords
5JBX 1.1 Å EC: 4.2.1.55 CRYSTAL STRUCTURE OF LIUC IN COMPLEX WITH COENZYME A AND MAL MYXOCOCCUS XANTHUS (STRAIN DK 1622) DEHYDRATASE ISOVALERATE MYXOCOCCUS XANTHUS LYASE
Ref.: THE STRUCTURE OF LIUC, A 3-HYDROXY-3-METHYLGLUTACON DEHYDRATASE INVOLVED IN ISOVALERYL-COA BIOSYNTHESIS MYXOCOCCUS XANTHUS, REVEALS INSIGHTS INTO SPECIFICI CATALYSIS. CHEMBIOCHEM V. 17 1658 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
COA B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
767.534 C21 H36 N7 O16 P3 S CC(C)...
MLI A:302;
B:303;
B:302;
B:304;
Valid;
Invalid;
Valid;
Invalid;
none;
none;
Atoms found MORE than expected: % Diff = 2;
none;
submit data
102.046 C3 H2 O4 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JBX 1.1 Å EC: 4.2.1.55 CRYSTAL STRUCTURE OF LIUC IN COMPLEX WITH COENZYME A AND MAL MYXOCOCCUS XANTHUS (STRAIN DK 1622) DEHYDRATASE ISOVALERATE MYXOCOCCUS XANTHUS LYASE
Ref.: THE STRUCTURE OF LIUC, A 3-HYDROXY-3-METHYLGLUTACON DEHYDRATASE INVOLVED IN ISOVALERYL-COA BIOSYNTHESIS MYXOCOCCUS XANTHUS, REVEALS INSIGHTS INTO SPECIFICI CATALYSIS. CHEMBIOCHEM V. 17 1658 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JBX - MLI C3 H2 O4 C(C(=O)[O-....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JBX - MLI C3 H2 O4 C(C(=O)[O-....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JBX - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: COA; Similar ligands found: 197
No: Ligand ECFP6 Tc MDL keys Tc
1 COA 1 1
2 0T1 0.894737 0.976744
3 DCA 0.893805 0.954023
4 COS 0.887931 0.977012
5 ETB 0.877193 0.920455
6 CAO 0.871795 0.965909
7 AMX 0.871795 0.988235
8 30N 0.871795 0.913979
9 CMX 0.864407 0.976744
10 SCO 0.864407 0.976744
11 FAM 0.857143 0.954545
12 ACO 0.857143 0.965909
13 FCX 0.857143 0.94382
14 HAX 0.85 0.954545
15 3KK 0.842975 0.977012
16 FYN 0.842975 1
17 CA6 0.836066 0.885417
18 SOP 0.836066 0.977012
19 MCD 0.836066 0.954545
20 COK 0.836066 0.977012
21 OXK 0.836066 0.977012
22 NMX 0.829268 0.903226
23 CO6 0.829268 0.977012
24 CMC 0.829268 0.977012
25 1VU 0.829268 0.965909
26 CAJ 0.822581 0.954545
27 SCD 0.822581 0.976744
28 2MC 0.822581 0.934066
29 2CP 0.81746 0.965909
30 BCO 0.816 0.977012
31 3HC 0.816 0.988372
32 1HE 0.816 0.955056
33 MLC 0.816 0.977012
34 A1S 0.816 0.977012
35 IVC 0.816 0.988372
36 COD 0.810345 0.988235
37 CAA 0.809524 0.988372
38 COO 0.809524 0.977012
39 MCA 0.809524 0.965909
40 YE1 0.809524 0.965517
41 SCA 0.80315 0.977012
42 MC4 0.80315 0.923913
43 IRC 0.796875 0.988372
44 3CP 0.796875 0.977012
45 CA8 0.796875 0.885417
46 BYC 0.796875 0.977012
47 COW 0.796875 0.965909
48 2KQ 0.796875 0.955056
49 COF 0.796875 0.955056
50 HGG 0.796875 0.977012
51 1GZ 0.796875 0.965909
52 4CA 0.790698 0.965909
53 FAQ 0.790698 0.977012
54 BCA 0.790698 0.965909
55 GRA 0.784615 0.977012
56 HXC 0.784615 0.955056
57 1CV 0.781955 0.977012
58 TGC 0.778626 0.965909
59 1CZ 0.772727 0.965909
60 CO8 0.772727 0.955056
61 S0N 0.772727 0.954545
62 2NE 0.772727 0.955056
63 CIC 0.772727 0.977012
64 0FQ 0.766917 0.977012
65 ST9 0.766917 0.955056
66 4CO 0.766917 0.965909
67 UCC 0.766917 0.955056
68 MFK 0.766917 0.955056
69 DCC 0.766917 0.955056
70 MYA 0.766917 0.955056
71 5F9 0.766917 0.955056
72 01A 0.761194 0.934066
73 0ET 0.761194 0.955056
74 CS8 0.755556 0.944444
75 WCA 0.755556 0.955056
76 4KX 0.75 0.944444
77 UOQ 0.75 0.955056
78 NHW 0.75 0.955056
79 HDC 0.75 0.955056
80 NHM 0.75 0.955056
81 HFQ 0.744526 0.955056
82 MRS 0.744526 0.955056
83 MRR 0.744526 0.955056
84 DAK 0.73913 0.944444
85 YNC 0.73913 0.965909
86 8Z2 0.733813 0.944444
87 NHQ 0.723404 0.988372
88 1HA 0.713287 0.955056
89 01K 0.708333 0.977012
90 COT 0.703448 0.977012
91 CCQ 0.695652 0.934066
92 CA3 0.693878 0.977012
93 CA5 0.671053 0.934066
94 UCA 0.666667 0.955056
95 93P 0.666667 0.965909
96 CO7 0.664234 0.977012
97 93M 0.64557 0.965909
98 OXT 0.634146 0.913979
99 5TW 0.607143 0.913979
100 4BN 0.607143 0.913979
101 PAP 0.603604 0.811765
102 JBT 0.598837 0.894737
103 BSJ 0.592814 0.944444
104 HMG 0.581081 0.943182
105 COA MYR 0.573333 0.922222
106 PLM COA 0.573333 0.922222
107 COA PLM 0.573333 0.922222
108 A3P 0.54955 0.8
109 PPS 0.547009 0.752688
110 0WD 0.521739 0.788889
111 RFC 0.490683 0.955056
112 SFC 0.490683 0.955056
113 191 0.490196 0.865979
114 3AM 0.482143 0.788235
115 PTJ 0.48062 0.872093
116 ACE SER ASP ALY THR NH2 COA 0.478261 0.932584
117 4PS 0.477477 0.682353
118 A22 0.468254 0.813953
119 A2D 0.465517 0.802326
120 PUA 0.462585 0.820225
121 PAJ 0.460938 0.883721
122 AGS 0.459016 0.806818
123 SAP 0.459016 0.806818
124 ATR 0.459016 0.8
125 3OD 0.458015 0.825581
126 ADP 0.453782 0.823529
127 A2R 0.448819 0.813953
128 BA3 0.445378 0.802326
129 NA7 0.442748 0.858824
130 OAD 0.442748 0.825581
131 ATP 0.442623 0.823529
132 AP5 0.441667 0.802326
133 B4P 0.441667 0.802326
134 APR 0.439024 0.802326
135 5FA 0.439024 0.823529
136 2A5 0.439024 0.847059
137 AQP 0.439024 0.823529
138 AR6 0.439024 0.802326
139 AN2 0.438017 0.813953
140 48N 0.435714 0.808989
141 M33 0.434426 0.813953
142 SRP 0.429688 0.837209
143 ANP 0.428571 0.804598
144 ADQ 0.427481 0.804598
145 YLB 0.426573 0.908046
146 YLP 0.425532 0.886364
147 5AL 0.425197 0.813953
148 7D3 0.425 0.793103
149 AD9 0.424 0.804598
150 APU 0.423611 0.786517
151 7D4 0.422764 0.793103
152 CA0 0.422764 0.804598
153 25L 0.422222 0.813953
154 ATF 0.421875 0.795455
155 NJP 0.421769 0.806818
156 A2P 0.421488 0.788235
157 A A A 0.421053 0.813953
158 8QN 0.419847 0.813953
159 PNS 0.419643 0.682353
160 ACP 0.419355 0.825581
161 NDP 0.417808 0.788889
162 ACQ 0.417323 0.825581
163 A1R 0.416667 0.882353
164 ATP A A A 0.416058 0.770115
165 A 0.415254 0.8
166 AMP 0.415254 0.8
167 FYA 0.414815 0.813953
168 1ZZ 0.414815 0.842697
169 TXA 0.414815 0.816092
170 NB8 0.414815 0.808989
171 AHX 0.413534 0.829545
172 DLL 0.413534 0.793103
173 00A 0.413534 0.758242
174 PAX 0.412903 0.793478
175 OMR 0.409722 0.853933
176 25A 0.409091 0.802326
177 OOB 0.409091 0.793103
178 NPW 0.408163 0.822222
179 WAQ 0.407407 0.860465
180 A A 0.407407 0.781609
181 TAT 0.40625 0.816092
182 4AD 0.406015 0.827586
183 AMO 0.406015 0.837209
184 YAP 0.405797 0.806818
185 FA5 0.405797 0.816092
186 TXP 0.405405 0.829545
187 ABM 0.404959 0.781609
188 PRX 0.404762 0.825581
189 ME8 0.404412 0.842697
190 BIS 0.404412 0.818182
191 AFH 0.404255 0.78022
192 J7V 0.403846 0.778947
193 NAI 0.402778 0.777778
194 ODP 0.402685 0.78022
195 ADX 0.4 0.752688
196 SRA 0.4 0.784091
197 AU1 0.4 0.804598
Ligand no: 2; Ligand: MLI; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 MLI 1 1
2 OAA 0.5 0.666667
3 SIN 0.5 0.785714
4 OXL 0.416667 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5jbx.bio1) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5jbx.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5JBX; Ligand: COA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5jbx.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5JBX; Ligand: COA; Similar sites found: 36
This union binding pocket(no: 4) in the query (biounit: 5jbx.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4N9Z V3L 0.009752 0.44088 1.91571
2 1TZD ADP 0.004507 0.43847 1.91571
3 1W2D ADP 0.003851 0.4319 1.91571
4 2AWN ADP 0.02795 0.40048 2.29885
5 5F90 LMR 0.007714 0.42729 2.5641
6 5F90 GLA GAL 0.007725 0.4261 2.5641
7 5F90 GLA GAL BGC 5VQ 0.02412 0.4005 2.5641
8 1ON3 MCA 0.00008684 0.49486 2.68199
9 2IF8 ADP 0.01287 0.4153 3.06513
10 2PUL ACP 0.007945 0.40475 3.06513
11 5DZT AMP 0.02741 0.40069 3.06513
12 5EVY SAL 0.02177 0.40495 3.83142
13 2XMY CDK 0.04066 0.40447 3.83142
14 4JGT PYR 0.03427 0.40329 3.83142
15 1YXM ADE 0.004166 0.44868 4.21456
16 1KUJ MMA 0.009573 0.40294 4.51128
17 3X01 AMP 0.002738 0.4521 4.5977
18 4CS9 AMP 0.01277 0.40499 5.29101
19 5MW8 ATP 0.008093 0.40274 6.89655
20 5HVJ ANP 0.0208 0.4027 6.89655
21 4XAQ 40F 0.01526 0.40298 7.27969
22 4KZV TRE 0.01704 0.41172 7.46269
23 5IN3 G1P 0.02124 0.40226 8.04598
24 5XG5 A2G 0.02355 0.40152 8.27586
25 3S6X SIA GAL BGC 0.01966 0.40716 8.81226
26 2NP9 YE1 0.000001232 0.46008 17.2414
27 2HK9 ATR 0.009496 0.41296 17.8182
28 1SG4 CO8 0.0000004012 0.51063 30.7692
29 1NZY BCA 0.0000000289 0.65422 39.8467
30 1JXZ BCA 0.00000003715 0.64934 40.2299
31 4QIJ 1HA 0.0000006318 0.65447 41.3793
32 4I42 1HA 0.0000003354 0.6527 45.977
33 4I4Z 2NE 0.00000004024 0.53053 45.977
34 2VSU ACO 0.00000000115 0.67917 47.5096
35 2VSS ACO 0.00000000208 0.66869 47.5096
36 1DUB CAA 0.000000009551 0.40244 49.4253
Pocket No.: 5; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found: 26
This union binding pocket(no: 5) in the query (biounit: 5jbx.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U7Z PMT 0.04889 0.40243 None
2 4OUC 5ID 0.002672 0.40186 1.91571
3 1RJD SAM 0.02573 0.40324 2.29885
4 1YQC GLV 0.0005631 0.45023 2.94118
5 3RSC TYD 0.008993 0.42684 3.06513
6 3TKY SAH 0.01327 0.41642 3.06513
7 5V49 MET 0.007468 0.40564 3.06513
8 2CWH NDP 0.03574 0.40537 3.06513
9 2NYR SVR 0.03522 0.40323 3.06513
10 1Q8Y ADP 0.009429 0.42404 3.83142
11 1FEC FAD 0.04299 0.41699 3.83142
12 3OIX FMN 0.01755 0.41501 3.83142
13 5TDF 7A3 0.005569 0.43187 4.98084
14 1N62 MCN 0.01657 0.43119 4.98084
15 1N62 FAD 0.04736 0.40803 4.98084
16 3HIW C2X 0.03096 0.40061 5.01931
17 2X1L MET 0.009663 0.40241 5.36398
18 2O4C NAD 0.03405 0.40883 6.13027
19 4WZ8 3W7 0.01597 0.43687 6.51341
20 3LQV ADE 0.008254 0.40499 6.95652
21 1P6O HPY 0.006046 0.41563 9.31677
22 1ZPR CB3 0.02052 0.40312 13.41
23 1WDK N8E 0.00001818 0.45872 37.931
24 4I42 1HA 0.0263 0.41251 45.977
25 2VSS V55 0.00007625 0.51764 47.5096
26 2VSU V55 0.0001613 0.49532 47.5096
Pocket No.: 6; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5jbx.bio1) has 1 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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