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Receptor
PDB id Resolution Class Description Source Keywords
1H16 1.53 Å EC: 2.3.1.54 PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH PYRUVATE AND COA ESCHERICHIA COLI LYASE GLYCYL RADICAL ENZYME TRANSFERASE ACYLTRANSFERASE
Ref.: X-RAY STRUCTURE OF PYRUVATE FORMATE-LYASE IN COMPLE PYRUVATE AND COA.HOW THE ENZYME USES THE CYS-418 TH RADICAL FOR PYRUVATE CLEAVAGE J.BIOL.CHEM. V. 277 40036 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
COA A:1000;
Valid;
none;
submit data
767.534 C21 H36 N7 O16 P3 S CC(C)...
DTL A:9009;
A:9010;
Valid;
Valid;
none;
none;
submit data
122.12 C4 H10 O4 C([C@...
MG A:9008;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
NA A:9001;
A:9002;
A:9003;
A:9004;
A:9005;
A:9006;
A:9007;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
PG4 A:9011;
A:9012;
A:9013;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
194.226 C8 H18 O5 C(COC...
PYR A:1001;
Valid;
none;
submit data
88.062 C3 H4 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1H16 1.53 Å EC: 2.3.1.54 PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH PYRUVATE AND COA ESCHERICHIA COLI LYASE GLYCYL RADICAL ENZYME TRANSFERASE ACYLTRANSFERASE
Ref.: X-RAY STRUCTURE OF PYRUVATE FORMATE-LYASE IN COMPLE PYRUVATE AND COA.HOW THE ENZYME USES THE CYS-418 TH RADICAL FOR PYRUVATE CLEAVAGE J.BIOL.CHEM. V. 277 40036 2002
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1H17 - DTL C4 H10 O4 C([C@@H]([....
2 1H18 - PYR C3 H4 O3 CC(=O)C(=O....
3 1H16 - DTL C4 H10 O4 C([C@@H]([....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1H17 - DTL C4 H10 O4 C([C@@H]([....
2 1H18 - PYR C3 H4 O3 CC(=O)C(=O....
3 1H16 - DTL C4 H10 O4 C([C@@H]([....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1H17 - DTL C4 H10 O4 C([C@@H]([....
2 1H18 - PYR C3 H4 O3 CC(=O)C(=O....
3 1H16 - DTL C4 H10 O4 C([C@@H]([....
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: DTL; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 DTL 1 1
2 MRY 1 1
3 03W 0.615385 0.791667
4 SOR 0.533333 0.954545
5 RB0 0.533333 0.913043
6 XYL 0.533333 0.913043
7 MTL 0.533333 0.954545
8 GOL 0.5 0.863636
Ligand no: 3; Ligand: PYR; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 F50 0.428571 0.6
5 2KT 0.411765 0.733333
6 AAE 0.411765 0.625
7 KIV 0.411765 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1H16; Ligand: COA; Similar sites found with APoc: 15
This union binding pocket(no: 1) in the query (biounit: 1h16.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 5LX9 OLB 2.60586
3 1WMA AB3 3.98551
4 2GWH PCI 4.02685
5 1GEG GLC 5.07812
6 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 5.85774
7 1J78 OLA 7.64192
8 1NU4 MLA 9.27835
9 4OGQ 7PH 16.129
10 5IXB LGA 17.5926
11 5ZCO CHD 18.6441
12 5Z84 CHD 18.6441
13 5W97 CHD 18.6441
14 2Y69 CHD 23.8095
15 1M2Z BOG 47.619
Pocket No.: 2; Query (leader) PDB : 1H16; Ligand: COA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1h16.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1H16; Ligand: DTL; Similar sites found with APoc: 7
This union binding pocket(no: 3) in the query (biounit: 1h16.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 6C8T EQJ 3.19149
2 6C92 EQJ 3.19149
3 1RWQ 5AP 4.12088
4 2I5F 5IP 9.17431
5 8CAT NDP 11.8577
6 5LXT 7AK 21.6783
7 5LXT GDP 21.6783
Pocket No.: 4; Query (leader) PDB : 1H16; Ligand: DTL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1h16.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1H16; Ligand: PYR; Similar sites found with APoc: 47
This union binding pocket(no: 5) in the query (biounit: 1h16.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2O1S TDP 1.28824
2 5ZQS BXP 1.47874
3 3LN0 52B 1.53322
4 2D3M COA 1.97044
5 5XWV 8H6 2.01613
6 2EXK XYS XYS 2.05607
7 3H4V DVP 2.08333
8 3H4V NAP 2.08333
9 5JOX EDG 2.13178
10 5KOR GDP 2.30326
11 5MR6 FAD 2.66344
12 2YAB AMP 2.77008
13 4IWN GEK 3.05677
14 3RI1 3RH 3.19489
15 2NVA PL2 3.22581
16 3MPI GRA 3.52645
17 1MXH NAP 3.62319
18 5Z5I XYS 3.68324
19 5Z5I FUB 3.68324
20 1IM8 SAI 3.68852
21 4PNI KQQ 3.92157
22 2ZCQ B65 4.09556
23 5CMK GLU 5.01931
24 1SZO CAX 5.83658
25 3RMK BML 6.0241
26 2HKA C3S 6.15385
27 2CJF RP4 6.36943
28 3IS2 FAD 6.49351
29 4H07 IPH 6.49351
30 4BFM ANP 6.58683
31 3D91 REM 6.74487
32 2J5S KTA 6.84411
33 1NE6 SP1 7.06714
34 5LI9 ACP 7.14286
35 1XI9 PLP 7.88177
36 5A6N U7E 9.18728
37 4O4K 2PK 10.4167
38 2WCJ M21 10.6383
39 4R38 RBF 10.7143
40 5IXG OTP 11.2426
41 5ODT ADP 12.0141
42 2AX9 BHM 12.5
43 2FR3 REA 14.5985
44 2YAJ 4HP 28.9855
45 5A0U CHT 30.9618
46 5FAW CHT 31.6206
47 3CXH SMA 35.7143
Pocket No.: 6; Query (leader) PDB : 1H16; Ligand: PYR; 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: 1h16.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1H16; Ligand: DTL; Similar sites found with APoc: 32
This union binding pocket(no: 7) in the query (biounit: 1h16.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 2GCE SFC 1.66667
2 4QS9 BGC 2.1097
3 5H2D ERG 2.52874
4 6HTO MET 3.25
5 6HTO 5AD 3.25
6 5CB3 APR 3.82514
7 5LAU AR6 3.84615
8 2IBN I1N 4
9 2VZZ SCA 4.12844
10 1VPE ANP 4.27136
11 4DHY GLC 4.47761
12 1PHP ADP 4.56853
13 2YVF NAD 4.65686
14 4TX6 38B 4.83871
15 1V6A TRE 5.12048
16 1QPG MAP 5.78313
17 5KVS 6XR 6.23377
18 5KVS NAP 6.23377
19 3PXP MYR 6.50685
20 2X06 NAD 6.97674
21 1N62 FAD 7.22892
22 2JDC CAO 7.53425
23 4XGX ADP 7.64706
24 1I1Q TRP 8.33333
25 4IQY AR6 8.75
26 2ZE7 AMP 9.09091
27 2ZE7 DST 9.09091
28 4RXH PRO PRO LYS LYS LYS ARG LYS VAL 9.29293
29 3POT TP7 12.8514
30 3POT TXZ 12.8514
31 3POT COM 12.8514
32 4NTM 2K8 16.5289
Pocket No.: 8; Query (leader) PDB : 1H16; Ligand: DTL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1h16.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
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