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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 LESS than expected: % Diff = 0;
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 (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1DUB Ki = 1.6 uM CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
2 1EY3 - DAK C32 H47 N8 O17 P3 S CC(C)(CO[P....
3 1MJ3 - HXC C27 H46 N7 O17 P3 S CCCCCC(=O)....
4 2DUB - CO8 C29 H50 N7 O17 P3 S CCCCCCCC(=....
5 5ZAI - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
6 5DTW Kd = 3.5 uM 5F9 C41 H74 N7 O17 P3 S CCCCCCCCCC....
7 5JBX - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: COA; Similar ligands found: 211
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 AMX 0.871795 0.988235
7 30N 0.871795 0.913979
8 CAO 0.871795 0.965909
9 CMX 0.864407 0.976744
10 SCO 0.864407 0.976744
11 ACO 0.857143 0.965909
12 FCX 0.857143 0.94382
13 FAM 0.857143 0.954545
14 HAX 0.85 0.954545
15 3KK 0.842975 0.977012
16 FYN 0.842975 1
17 SOP 0.836066 0.977012
18 MCD 0.836066 0.954545
19 OXK 0.836066 0.977012
20 CA6 0.836066 0.885417
21 COK 0.836066 0.977012
22 CO6 0.829268 0.977012
23 NMX 0.829268 0.903226
24 1VU 0.829268 0.965909
25 CMC 0.829268 0.977012
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 A1S 0.816 0.977012
31 3HC 0.816 0.988372
32 IVC 0.816 0.988372
33 1HE 0.816 0.955056
34 MLC 0.816 0.977012
35 BCO 0.816 0.977012
36 COD 0.810345 0.988235
37 COO 0.809524 0.977012
38 MCA 0.809524 0.965909
39 CAA 0.809524 0.988372
40 YE1 0.809524 0.965517
41 MC4 0.80315 0.923913
42 SCA 0.80315 0.977012
43 CA8 0.796875 0.885417
44 COF 0.796875 0.955056
45 BYC 0.796875 0.977012
46 COW 0.796875 0.965909
47 3CP 0.796875 0.977012
48 IRC 0.796875 0.988372
49 1GZ 0.796875 0.965909
50 HGG 0.796875 0.977012
51 2KQ 0.796875 0.955056
52 BCA 0.790698 0.965909
53 4CA 0.790698 0.965909
54 FAQ 0.790698 0.977012
55 HXC 0.784615 0.955056
56 GRA 0.784615 0.977012
57 1CV 0.781955 0.977012
58 TGC 0.778626 0.965909
59 2NE 0.772727 0.955056
60 1CZ 0.772727 0.965909
61 CO8 0.772727 0.955056
62 S0N 0.772727 0.954545
63 CIC 0.772727 0.977012
64 DCC 0.766917 0.955056
65 UCC 0.766917 0.955056
66 0FQ 0.766917 0.977012
67 MYA 0.766917 0.955056
68 ST9 0.766917 0.955056
69 4CO 0.766917 0.965909
70 5F9 0.766917 0.955056
71 MFK 0.766917 0.955056
72 01A 0.761194 0.934066
73 0ET 0.761194 0.955056
74 WCA 0.755556 0.955056
75 CS8 0.755556 0.944444
76 UOQ 0.75 0.955056
77 NHW 0.75 0.955056
78 NHM 0.75 0.955056
79 4KX 0.75 0.944444
80 HDC 0.75 0.955056
81 MRR 0.744526 0.955056
82 MRS 0.744526 0.955056
83 HFQ 0.744526 0.955056
84 YNC 0.73913 0.965909
85 DAK 0.73913 0.944444
86 8Z2 0.733813 0.944444
87 NHQ 0.723404 0.988372
88 F8G 0.715278 0.913979
89 1HA 0.713287 0.955056
90 01K 0.708333 0.977012
91 COT 0.703448 0.977012
92 CCQ 0.695652 0.934066
93 CA3 0.693878 0.977012
94 7L1 0.692308 0.965909
95 CA5 0.671053 0.934066
96 UCA 0.666667 0.955056
97 93P 0.666667 0.965909
98 CO7 0.664234 0.977012
99 93M 0.64557 0.965909
100 OXT 0.634146 0.913979
101 5TW 0.607143 0.913979
102 4BN 0.607143 0.913979
103 PAP 0.603604 0.811765
104 JBT 0.598837 0.894737
105 BSJ 0.592814 0.944444
106 HMG 0.581081 0.943182
107 COA PLM 0.573333 0.922222
108 PLM COA 0.573333 0.922222
109 A3P 0.54955 0.8
110 PPS 0.547009 0.752688
111 ASP ASP ASP ILE CMC NH2 0.536585 0.932584
112 0WD 0.521739 0.788889
113 SFC 0.490683 0.955056
114 RFC 0.490683 0.955056
115 191 0.490196 0.865979
116 ACE SER ASP ALY THR NH2 COA 0.483333 0.932584
117 3AM 0.482143 0.788235
118 PTJ 0.48062 0.872093
119 4PS 0.477477 0.682353
120 A22 0.468254 0.813953
121 A2D 0.465517 0.802326
122 PUA 0.462585 0.820225
123 PAJ 0.460938 0.883721
124 ATR 0.459016 0.8
125 SAP 0.459016 0.806818
126 AGS 0.459016 0.806818
127 3OD 0.458015 0.825581
128 ADP 0.453782 0.823529
129 A2R 0.448819 0.813953
130 BA3 0.445378 0.802326
131 OAD 0.442748 0.825581
132 NA7 0.442748 0.858824
133 ATP 0.442623 0.823529
134 HEJ 0.442623 0.823529
135 AP5 0.441667 0.802326
136 B4P 0.441667 0.802326
137 AR6 0.439024 0.802326
138 APR 0.439024 0.802326
139 2A5 0.439024 0.847059
140 5FA 0.439024 0.823529
141 AQP 0.439024 0.823529
142 AN2 0.438017 0.813953
143 AT4 0.438017 0.816092
144 48N 0.435714 0.808989
145 M33 0.434426 0.813953
146 9X8 0.431818 0.806818
147 SRP 0.429688 0.837209
148 ANP 0.428571 0.804598
149 ADQ 0.427481 0.804598
150 YLB 0.426573 0.908046
151 YLP 0.425532 0.886364
152 5AL 0.425197 0.813953
153 7D3 0.425 0.793103
154 AD9 0.424 0.804598
155 APU 0.423611 0.786517
156 7D4 0.422764 0.793103
157 CA0 0.422764 0.804598
158 25L 0.422222 0.813953
159 ATF 0.421875 0.795455
160 F2R 0.421769 0.865169
161 NJP 0.421769 0.806818
162 A2P 0.421488 0.788235
163 A A A 0.421053 0.813953
164 8QN 0.419847 0.813953
165 PNS 0.419643 0.682353
166 ACP 0.419355 0.825581
167 NDP 0.417808 0.788889
168 ACQ 0.417323 0.825581
169 A1R 0.416667 0.882353
170 ATP A A A 0.416058 0.770115
171 A 0.415254 0.8
172 AMP 0.415254 0.8
173 1ZZ 0.414815 0.842697
174 NB8 0.414815 0.808989
175 TXA 0.414815 0.816092
176 FYA 0.414815 0.813953
177 DLL 0.413534 0.793103
178 00A 0.413534 0.758242
179 AHX 0.413534 0.829545
180 PAX 0.412903 0.793478
181 DQV 0.411348 0.813953
182 OMR 0.409722 0.853933
183 9ZD 0.409091 0.818182
184 25A 0.409091 0.802326
185 OOB 0.409091 0.793103
186 9ZA 0.409091 0.818182
187 NPW 0.408163 0.822222
188 6YZ 0.407692 0.825581
189 A A 0.407407 0.781609
190 WAQ 0.407407 0.860465
191 TAT 0.40625 0.816092
192 T99 0.40625 0.816092
193 AMO 0.406015 0.837209
194 4AD 0.406015 0.827586
195 A3R 0.406015 0.882353
196 FA5 0.405797 0.816092
197 YAP 0.405797 0.806818
198 B5Y 0.405797 0.786517
199 TXP 0.405405 0.829545
200 ABM 0.404959 0.781609
201 PRX 0.404762 0.825581
202 ME8 0.404412 0.842697
203 BIS 0.404412 0.818182
204 AFH 0.404255 0.78022
205 J7V 0.403846 0.778947
206 NAI 0.402778 0.777778
207 ODP 0.402685 0.78022
208 DAL AMP 0.401515 0.793103
209 AU1 0.4 0.804598
210 ADX 0.4 0.752688
211 SRA 0.4 0.784091
Ligand no: 2; Ligand: MLI; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 MLI 1 1
2 OAA 0.5 0.666667
3 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 with APoc: 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 Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found with APoc: 131
This union binding pocket(no: 2) in the query (biounit: 5jbx.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZGD NAP 0.766284
2 4K49 HFQ 1.47059
3 6G33 5ID 1.53257
4 3PCR GTP 1.85185
5 4OUC 5ID 1.91571
6 6G34 5ID 1.91571
7 6BCA GSP 2.16216
8 4P6G 2FZ 2.21239
9 5J6D 6H5 2.29885
10 4Q9N NAI 2.29885
11 1YAG ATP 2.29885
12 2BII MTV 2.29885
13 1G60 SAM 2.30769
14 6GBC AMP 2.68199
15 5M67 NAD 2.68199
16 5M67 3D1 2.68199
17 1PN4 HDC 2.68199
18 4HXY NDP 2.68199
19 2NVA PL2 2.68199
20 4QNW FMN 2.68199
21 4ZCW 4NG 2.68199
22 1JG3 ADN 2.97872
23 3RSC TYD 3.06513
24 3IAA TYD 3.06513
25 5V49 MET 3.06513
26 2OEM 1AE 3.06513
27 2CWH PYC 3.06513
28 2CWH NDP 3.06513
29 5V49 8WA 3.06513
30 2G50 ALA 3.06513
31 1BH2 GSP 3.06513
32 4BLW SAH 3.06513
33 4YFY 1YJ 3.44828
34 1OVD ORO 3.44828
35 4IX4 ADP 3.44828
36 1OVD FMN 3.44828
37 1EP2 ORO 3.44828
38 3C6K MTA 3.44828
39 3C6K SPD 3.44828
40 1RM4 NDP 3.44828
41 1Z2I NAD 3.44828
42 1EP2 FMN 3.44828
43 1EK0 GNP 3.52941
44 1Q8Y ADP 3.83142
45 5ERR ADP 3.83142
46 4JGT PYR 3.83142
47 3OIX FMN 3.83142
48 2FR6 URI 4.10959
49 2FR6 CTN 4.10959
50 4CTA ATP 4.21456
51 4EU7 CIT 4.21456
52 4EU7 COA 4.21456
53 4UUW AMP 4.21456
54 2OFV 242 4.21456
55 3TDC 0EU 4.21456
56 1V97 MTE 4.5977
57 2A42 ATP 4.61538
58 3R35 4CO 4.63576
59 5EE5 GTP 4.67836
60 1UPT GTP 4.67836
61 1N62 MCN 4.98084
62 1LDN NAD 4.98084
63 3V2U GLA 4.98084
64 1LDN OXM 4.98084
65 3WQT ANP 4.98084
66 3MJY IJZ 5.36398
67 3MJY FMN 5.36398
68 5XFV FMN 5.36398
69 4ZY1 4U5 5.36398
70 3C3N FMN 5.36398
71 4WZH FMN 5.36398
72 2GSD NAD 5.36398
73 1EBG PAH 5.36398
74 5THZ SAH 5.36398
75 4R6W SAH 5.42636
76 6BCB GSP 5.47945
77 1PNO NAP 5.55556
78 4LCN GNG 5.58376
79 2A5F GTP 5.69948
80 5LXT ACP 5.74713
81 2OOR TXP 5.74713
82 5O2D 9HH 6
83 5EJL C2E 6.04839
84 2O4C NAD 6.13027
85 2XTZ GSP 6.13027
86 3HRD MCN 6.13027
87 1DAK ADP 6.25
88 1DAK DPU 6.25
89 4WZ8 3W7 6.51341
90 2X24 X24 6.51341
91 4ZOH MCN 6.54762
92 5MW8 ATP 6.89655
93 3LQV ADE 6.95652
94 2C9O ADP 7.27969
95 5Y6Q MCN 8.02469
96 1T3Q MCN 8.04598
97 1T3Q FAD 8.04598
98 5U5G NAP 8.04598
99 5AG3 3EB 8.04598
100 5LUN ARG 8.04598
101 4NG2 OHN 8.69565
102 4CL6 7SB 8.77193
103 2MBR EPU 8.81226
104 1RM0 NAI 8.81226
105 4ZM4 P3B 9.1954
106 1P6O HPY 9.31677
107 4MCC 21X 9.34959
108 4Y8D 49J 10.7143
109 6APL C5P 10.728
110 5JWC FAD 10.9405
111 6EDK 1YA 11.0599
112 5W4W 9WG 11.1111
113 4KBA 1QM 11.1111
114 1FFU CDP 11.1111
115 4OOP DUP 12.0482
116 2D0O ADP 12.2605
117 3P48 DUP 12.9252
118 5LXM ADP 13.1579
119 3KLJ FAD 13.41
120 1ZPR CB3 13.41
121 3EYA TDP 13.7931
122 5G5G MCN 16.8582
123 2NP9 YE1 17.2414
124 6DA9 FMN 18.0077
125 1SG4 CO8 30.7692
126 2W83 GTP 35.0649
127 1WDK N8E 37.931
128 4IZC 1GZ 42.1456
129 4I4Z 2NE 45.977
130 2VSS V55 47.5096
131 2VSU V55 47.5096
Pocket No.: 3; Query (leader) PDB : 5JBX; Ligand: COA; Similar sites found with APoc: 67
This union binding pocket(no: 3) in the query (biounit: 5jbx.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 3KP6 SAL None
3 3F9W SAH None
4 3ZO7 K6H None
5 1RJW ETF 1.53257
6 1TZD ADP 1.91571
7 1W2D ADP 1.91571
8 2V7O DRN 1.91571
9 4U03 TLL 1.91571
10 4U03 GTP 1.91571
11 5YJS SAL 1.91571
12 4C2V YJA 1.91571
13 2AWN ADP 2.29885
14 5F90 LMR 2.5641
15 5F90 GLA GAL 2.5641
16 1ON3 MCA 2.68199
17 5ME4 HP4 2.68199
18 1ZX5 LFR 2.68199
19 4XAR 40F 2.68199
20 4XV1 904 2.68199
21 2IF8 ADP 3.06513
22 5T63 ALA ALA ALA ALA 3.06513
23 1UCD U5P 3.15789
24 5DEY 59T 3.44828
25 4B7X NAP 3.44828
26 2VN9 GVD 3.83142
27 1Q8Y ADE 3.83142
28 5TQZ GLC 4
29 1YXM ADE 4.21456
30 1KUJ MMA 4.51128
31 3X01 AMP 4.5977
32 2BMB PMM 4.5977
33 1WOG 16D 4.5977
34 5FFF NAP 4.66926
35 3HCH RSM 4.79452
36 4CS9 AMP 5.29101
37 5OCQ CIT 5.36398
38 3FSY SCA 5.42169
39 5OES ADP 6.51341
40 5MW8 ATP 6.89655
41 4XAQ 40F 7.27969
42 1KC7 PPR 7.27969
43 3VC3 C6P 7.66284
44 6E8I PTR 8.28402
45 3KO0 TFP 8.91089
46 5HCY 60D 9.66767
47 2Q6B HR2 9.96169
48 5OKT 9XK 11.1111
49 5W4W 9WG 11.1111
50 4KBA 1QM 11.1111
51 3O94 NCA 11.3744
52 5GM1 SAH 13.0268
53 3WDM ADN 15.3257
54 2NP9 YE1 17.2414
55 4ZDC CO8 23.3716
56 1SG4 CO8 30.7692
57 4B3J COA 37.931
58 1WDK N8E 37.931
59 1NZY BCA 39.8467
60 1JXZ BCA 40.2299
61 4QIJ 1HA 41.3793
62 4IZC 1GZ 42.1456
63 4I42 1HA 45.977
64 4I4Z 2NE 45.977
65 2VSU ACO 47.5096
66 2VSS ACO 47.5096
67 5DUF G7A 48.659
Pocket No.: 4; Query (leader) PDB : 5JBX; Ligand: COA; Similar sites found with APoc: 31
This union binding pocket(no: 4) in the query (biounit: 5jbx.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZXE PGZ None
2 6EOM ALA LYS 1.91571
3 5NFB 8VT 2.27273
4 6GH9 MIX 2.29885
5 5F90 GLA GAL BGC 5VQ 2.5641
6 3RKR NAP 2.68199
7 2PUL ACP 3.06513
8 5DZT AMP 3.06513
9 5NCB JZ3 3.06513
10 3K1X DBX 3.07692
11 2BIF SIN 3.44828
12 5G3U FDA 3.44828
13 5EVY SAL 3.83142
14 2XMY CDK 3.83142
15 4JGT PYR 3.83142
16 3H4V NAP 3.83142
17 4JLS 3ZE 3.94737
18 6AC9 ANP 5.74713
19 2IID FAD 6.13027
20 2IID PHE 6.13027
21 5TS5 FAD 6.13027
22 5HVJ ANP 6.89655
23 4KZV TRE 7.46269
24 1TL2 NDG 7.62712
25 2WEL K88 8
26 5IN3 G1P 8.04598
27 5XG5 A2G 8.27586
28 3S6X SIA GAL BGC 8.81226
29 4WZA ACP 10.3448
30 5ZYN SIN 15.3257
31 2HK9 ATR 17.8182
Pocket No.: 5; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found with APoc: 66
This union binding pocket(no: 5) in the query (biounit: 5jbx.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4MG7 27H None
2 1U7Z PMT None
3 5ICE SAH 1.14943
4 6C5B SAH 2.29885
5 4RF7 ARG 2.29885
6 1E7S NAP 2.29885
7 1RJD SAM 2.29885
8 3THR C2F 2.68199
9 5X8I SQZ 2.89017
10 1YQC GLV 2.94118
11 3TKY SAH 3.06513
12 2C42 PYR 3.06513
13 2C42 TPP 3.06513
14 4WHZ 3NL 3.44828
15 4PU5 ANP 3.44828
16 4JJF N2I 3.44828
17 1NHZ 486 3.44828
18 1UPF URF 3.57143
19 1NVM NAD 3.83142
20 1FEC FAD 3.83142
21 1WP4 NDP 3.83142
22 4A1O JLN 4.21456
23 3AB1 FAD 4.21456
24 3IQE F42 4.21456
25 4Q9M FPP 4.47154
26 4A6D SAM 4.5977
27 2C49 ADN 4.5977
28 1NJJ ORX 4.5977
29 5TDF 7A3 4.98084
30 5EEH P9P 4.98084
31 5EEH SAH 4.98084
32 6GAS FAD 4.98084
33 1N62 FAD 4.98084
34 4PQG UDP 4.98084
35 5TE1 7A2 4.98084
36 3HIW C2X 5.01931
37 2X1L MET 5.36398
38 5CYV WCA 5.47945
39 6H3O FAD 5.74713
40 1GR0 NAD 5.74713
41 3RUG DB6 6.51341
42 4UCI SAM 6.89655
43 3AKK ADP 6.89655
44 2WOE AR6 6.89655
45 3HDY FAD 7.27969
46 3HDY GDU 7.27969
47 6F3M NAD 7.27969
48 3OU2 SAH 7.33945
49 3T1A 5MA 7.66284
50 1MQ0 BRD 8.57143
51 1VG0 GER 8.69565
52 3GF4 U5P 8.81226
53 3KO0 TFP 8.91089
54 3HUJ AGH 9.09091
55 4ZM4 PLP 9.1954
56 1T36 ADP 9.57854
57 5HZ9 5M8 9.62963
58 2H7C COA 9.96169
59 5XVH NAP 10.728
60 3DVA TPW 11.4943
61 1W85 TDP 11.4943
62 5AHS COA 12.2605
63 5X8G S0N 15.7088
64 5GK9 ACO 24
65 4QIJ 1HA 41.3793
66 4I42 1HA 45.977
Pocket No.: 6; Query (leader) PDB : 5JBX; Ligand: MLI; Similar sites found with APoc: 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 Sequence Similarity
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