Receptor
PDB id Resolution Class Description Source Keywords
6MDF 2.46 Å EC: 2.7.1.36 MEVALONATE KINASE FROM METHANOSARCINA MAZEI WITH 5-PHOSPHOME BOUND METHANOSARCINA MAZEI KINASE TRANSFERASE
Ref.: STRUCTURAL INSIGHT INTO SUBSTRATE AND PRODUCT BINDI ARCHAEAL MEVALONATE KINASE. PLOS ONE V. 13 08419 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:406;
A:402;
B:504;
B:502;
B:503;
B:507;
A:407;
A:403;
A:405;
B:505;
A:408;
B:506;
A:404;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
PMV A:401;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
228.137 C6 H13 O7 P C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6MDE 2.1 Å EC: 2.7.1.36 MEVALONATE KINASE FROM METHANOSARCINA MAZEI WITH MEVALONATE METHANOSARCINA MAZEI KINASE TRANSFERASE
Ref.: STRUCTURAL INSIGHT INTO SUBSTRATE AND PRODUCT BINDI ARCHAEAL MEVALONATE KINASE. PLOS ONE V. 13 08419 2018
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6MDE - MEV C6 H11 O4 C[C@@](CCO....
2 6MDF - PMV C6 H13 O7 P C[C@@](CCO....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6MDE - MEV C6 H11 O4 C[C@@](CCO....
2 6MDF - PMV C6 H13 O7 P C[C@@](CCO....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6MDE - MEV C6 H11 O4 C[C@@](CCO....
2 6MDF - PMV C6 H13 O7 P C[C@@](CCO....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PMV; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PMV 1 1
2 DP6 0.731707 1
3 1CO 0.5 0.625
4 3S4 0.431818 0.923077
5 MAH 0.428571 0.605263
6 BHI 0.425532 0.878049
7 FM0 0.411765 0.853659
Similar Ligands (3D)
Ligand no: 1; Ligand: PMV; Similar ligands found: 177
No: Ligand Similarity coefficient
1 DLT 0.9266
2 IPR 0.9213
3 DED 0.9193
4 PA5 0.9183
5 DMA 0.9174
6 EIP 0.9167
7 R10 0.9149
8 RP5 0.9148
9 IPE 0.9124
10 5RP 0.9085
11 R5P 0.9063
12 R52 0.9062
13 S6P 0.9061
14 TX4 0.9054
15 DX5 0.9051
16 LX1 0.9049
17 6FR 0.9048
18 2JA 0.9044
19 DXP 0.9031
20 RES 0.9030
21 SG3 0.9026
22 5SP 0.9025
23 D5X 0.9010
24 1PS 0.9007
25 H6P 0.8996
26 IS3 0.8985
27 ABH 0.8985
28 6HN 0.8978
29 D6P 0.8975
30 MLY 0.8974
31 6C4 0.8973
32 NFZ 0.8967
33 F6R 0.8965
34 10G 0.8964
35 DER 0.8957
36 4TP 0.8950
37 IJ6 0.8949
38 58X 0.8947
39 M3L 0.8944
40 DHH 0.8944
41 NPI 0.8944
42 RGP 0.8944
43 LXP 0.8944
44 PAL 0.8938
45 A5P 0.8937
46 GVA 0.8924
47 E4P 0.8916
48 DEZ 0.8915
49 CIR 0.8915
50 JFM 0.8914
51 ILO 0.8913
52 2JJ 0.8912
53 1AE 0.8902
54 PAN 0.8898
55 DA3 0.8896
56 5TO 0.8889
57 6C8 0.8874
58 HSX 0.8868
59 6PR 0.8860
60 F6P 0.8858
61 DHM 0.8856
62 10E 0.8854
63 ARG 0.8854
64 6C5 0.8853
65 0CN 0.8851
66 3CX 0.8850
67 PTB 0.8849
68 IVL 0.8849
69 DG2 0.8848
70 NLG 0.8848
71 SSC 0.8836
72 GRQ 0.8834
73 GGB 0.8833
74 KAP 0.8830
75 HSA 0.8830
76 UN1 0.8830
77 M6R 0.8827
78 0K2 0.8826
79 0CH 0.8826
80 HLP 0.8822
81 5OY 0.8820
82 AGP 0.8818
83 ATX 0.8816
84 IAR 0.8815
85 DAR 0.8815
86 JQ5 0.8808
87 JX7 0.8805
88 DST 0.8801
89 XOG 0.8798
90 ZZU 0.8796
91 0JX 0.8796
92 ABF 0.8795
93 F98 0.8790
94 G88 0.8790
95 P3S 0.8782
96 5WN 0.8782
97 GRF 0.8781
98 6FG 0.8779
99 PML 0.8778
100 NLQ 0.8773
101 TA6 0.8771
102 GHQ 0.8766
103 MP5 0.8766
104 1X4 0.8763
105 EXY 0.8763
106 AHL 0.8757
107 2OR 0.8757
108 MF3 0.8756
109 2E6 0.8753
110 ALY 0.8748
111 KNA 0.8748
112 0CJ 0.8733
113 ISY 0.8727
114 2E4 0.8718
115 G6Q 0.8715
116 5DL 0.8714
117 9J6 0.8712
118 F1X 0.8708
119 FOM 0.8708
120 S3P 0.8704
121 6MW 0.8702
122 64Z 0.8700
123 P93 0.8699
124 EGV 0.8698
125 0QA 0.8695
126 LPA 0.8693
127 BGP 0.8690
128 HPO 0.8686
129 TEG 0.8685
130 M1T 0.8681
131 26P 0.8680
132 6PG 0.8680
133 STX 0.8679
134 HAR 0.8675
135 OJD 0.8673
136 PUE 0.8672
137 5PV 0.8670
138 XRX 0.8669
139 DI6 0.8668
140 MGB 0.8658
141 KPC 0.8657
142 D8X 0.8654
143 TG6 0.8642
144 JF5 0.8638
145 API 0.8633
146 NNH 0.8633
147 ENW 0.8628
148 8SZ 0.8627
149 HCA 0.8623
150 MLZ 0.8620
151 9C2 0.8620
152 R1P 0.8616
153 9YT 0.8616
154 F63 0.8611
155 37E 0.8610
156 2NP 0.8608
157 OOG 0.8605
158 VUR 0.8604
159 LUQ 0.8603
160 4JK 0.8599
161 PAU 0.8598
162 11C 0.8589
163 5KJ 0.8582
164 Q06 0.8579
165 X1R 0.8576
166 HJH 0.8570
167 XI7 0.8567
168 PUW 0.8567
169 0CM 0.8565
170 P4F 0.8550
171 LGT 0.8539
172 NBB 0.8535
173 TU0 0.8535
174 C26 0.8535
175 CLT 0.8530
176 ING 0.8525
177 F1P 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6MDE; Ligand: MEV; 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: 6mde.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6MDE; Ligand: MEV; 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: 6mde.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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