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Receptor
PDB id Resolution Class Description Source Keywords
5J32 1.93 Å EC: 1.1.1.85 ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH ISOPROPYLMALAT ARABIDOPSIS THALIANA DEHYDROGENASE LEUCINE BIOSYNTHESIS GLUCOSINOLATE BIOSYNTHEOXIDOREDUCTASE
Ref.: STRUCTURE AND MECHANISM OF ISOPROPYLMALATE DEHYDROG FROM ARABIDOPSIS THALIANA: INSIGHTS ON LEUCINE AND GLUCOSINOLATE BIOSYNTHESIS. J.BIOL.CHEM. V. 291 13421 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:501;
C:501;
A:503;
C:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
IPM C:504;
C:502;
A:502;
A:504;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 8.3 uM
176.167 C7 H12 O5 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5J32 1.93 Å EC: 1.1.1.85 ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH ISOPROPYLMALAT ARABIDOPSIS THALIANA DEHYDROGENASE LEUCINE BIOSYNTHESIS GLUCOSINOLATE BIOSYNTHEOXIDOREDUCTASE
Ref.: STRUCTURE AND MECHANISM OF ISOPROPYLMALATE DEHYDROG FROM ARABIDOPSIS THALIANA: INSIGHTS ON LEUCINE AND GLUCOSINOLATE BIOSYNTHESIS. J.BIOL.CHEM. V. 291 13421 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5J32 Kd = 8.3 uM IPM C7 H12 O5 CC(C)[C@@H....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5J32 Kd = 8.3 uM IPM C7 H12 O5 CC(C)[C@@H....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4Y1P - IPM C7 H12 O5 CC(C)[C@@H....
2 1A05 - IPM C7 H12 O5 CC(C)[C@@H....
3 5J32 Kd = 8.3 uM IPM C7 H12 O5 CC(C)[C@@H....
4 3TY3 - GGG C6 H11 N3 O4 C(C(=O)NCC....
5 2Y42 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 2Y41 - IPM C7 H12 O5 CC(C)[C@@H....
7 1HEX Ki = 614.6 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 5HN6 - IPM C7 H12 O5 CC(C)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IPM; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 IPM 1 1
2 TAR 0.47619 0.8
3 TLA 0.47619 0.8
4 LAC 0.47619 0.631579
5 2OP 0.47619 0.631579
6 SRT 0.47619 0.8
7 LFC 0.428571 0.789474
8 LGT 0.416667 0.8
9 GAE 0.416667 0.8
10 RAT 0.416667 0.8
11 DXX 0.409091 0.7
12 3LR 0.4 0.625
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5J32; Ligand: IPM; Similar sites found with APoc: 150
This union binding pocket(no: 1) in the query (biounit: 5j32.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1HG4 LPP None
2 4WG0 CHD None
3 2AIB ERG None
4 1Q0H FOM 0.992556
5 5EK3 5PK 1.24069
6 3WXL ADP 1.24069
7 5JM8 ATP 1.24069
8 1TMX HGX 1.36519
9 4LSJ LSJ 1.55039
10 2QA8 GEN 1.55039
11 1M2Z DEX 1.55642
12 3BQD DAY 1.56863
13 4MG7 27H 1.56863
14 4P6X HCY 1.56863
15 5K13 6Q7 1.62602
16 1PK8 ATP 1.65877
17 5LOF 70R 1.73697
18 4NE2 SH2 1.79641
19 1LTH NAD 1.88088
20 5L7G 6QE 1.96721
21 2RH1 CAU 1.98511
22 4Z24 FAD 1.98511
23 2O4J VD4 2.05479
24 4UDB CV7 2.20588
25 5NWI TYR PHE SER SEP ASN 2.29008
26 4W4S B29 2.33333
27 3PXP MYR 2.39726
28 2OBF F83 2.42215
29 2C43 COA 2.47678
30 3OND ADN 2.48139
31 3NTD COA 2.48139
32 3NTA COA 2.48139
33 3NT6 COA 2.48139
34 5LGA 6VH 2.66667
35 5E7V M7E 2.66667
36 1DUV PSQ 2.7027
37 5TDF ADE 2.72953
38 1V8B NAD 2.72953
39 5A8E XTK 2.85714
40 4ZW9 BGC 2.97767
41 4ZW9 GLC 2.97767
42 6H3O FAD 2.97767
43 4KVL PLM 2.97767
44 1DKF OLA 3.00429
45 1DKF BMS 3.00429
46 3GKJ HC3 3.01724
47 4POJ 2VP 3.0303
48 4M8E 29V 3.0303
49 1SR7 MOF 3.0888
50 3HLX PQQ 3.10078
51 4OAR 2S0 3.10078
52 5NI5 8YB 3.125
53 3RY9 1CA 3.2
54 3NJ4 NAD 3.22581
55 4Q0A 4OA 3.31126
56 1ESM COA 3.48101
57 5NTW 98N 3.50195
58 4C2V YJA 3.50877
59 5G5W R8C 3.57143
60 2QZT PLM 3.6036
61 1O6U PLM 3.72208
62 1OLM VTQ 3.72208
63 5HZ5 65X 3.73134
64 1FCZ 156 3.82979
65 1NHZ 486 3.92857
66 5IXK 6EW 3.94737
67 2HW2 RFP 4.1958
68 1YUC EPH 4.31373
69 3Q8G PEE 4.375
70 4E2J MOF 4.4
71 3GN8 DEX 4.41767
72 5UFS 1TA 4.43548
73 3LN0 52B 4.4665
74 2YFT DQR 4.4665
75 5W7R 9Z7 4.4665
76 2YOO K2B 4.4665
77 4Q9M FPP 4.47154
78 4Q9M 2ZW 4.47154
79 3KP6 SAL 4.63576
80 1UOU CMU 4.71464
81 2A3I C0R 4.74308
82 2ZYJ PGU 4.78589
83 2Q1H AS4 4.8
84 3IPQ 965 4.947
85 2D5Z L35 4.96454
86 4NAT 2W5 5
87 4NAT ADP 5
88 1DB1 VDX 5.01931
89 5WIU AQD 5.21327
90 4OMJ 2TX 5.39568
91 4IAE 1DX 5.82011
92 5CXI 5TW 5.91133
93 1G2N EPH 6.06061
94 2R40 EPH 6.08365
95 4XCL AGS 6.17761
96 1DMH LIO 6.43087
97 1W2Y DUN 6.45161
98 1FK5 OLA 6.45161
99 1QIN GIP 6.55738
100 1ITW ICT 6.69975
101 3FAL LO2 6.76692
102 3UMV FAD 6.94789
103 4RW3 PLM 6.95364
104 5DEP UD1 6.97674
105 4XXH T6P 7.05882
106 3BEJ MUF 7.14286
107 3DCT 064 7.23404
108 1K7L 544 7.29167
109 5ICK FEZ 7.42358
110 1I7L ATP 7.44337
111 3KMR EQN 7.5188
112 3KMZ EQO 7.5188
113 1RDT L79 7.74648
114 3FEI CTM 7.86517
115 3KFC 61X 7.90514
116 1DTL BEP 8.07453
117 1FM9 9CR 8.08823
118 3H0A 9RA 8.08823
119 4AQL TXC 8.18859
120 1XVB BHL 8.23529
121 1XAP TTB 8.2397
122 6GMN F4E 8.24742
123 2BJ4 OHT 8.33333
124 5N1X 8HH 8.47458
125 2QO4 CHD 8.73016
126 2LBD REA 8.98876
127 1LRI CLR 9.18367
128 6DIO NAD 9.42928
129 5N7O 69Y 9.50226
130 4KBA 1QM 10.2719
131 2BP1 FLC 10.2778
132 5HZ9 5M8 10.3704
133 4US3 TRP 10.67
134 3D2Y AH0 ALA FGA LYS 10.728
135 2UXR ICT 10.9453
136 1MV8 NAD 11.1663
137 1MUU NAD 11.1663
138 2CJF RP4 11.465
139 3WCA FPS 12.6027
140 1VR0 3SL 12.9555
141 4YEF 4CQ 13.4831
142 5Z1N PEF 14.881
143 6ADI NDP 15.6328
144 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 16.4912
145 5CSD ACD 17.6101
146 2D4V FLC 42.928
147 1GRO ICT 42.928
148 1XKD ICT 43.1762
149 1HQS CIT 43.6725
150 3FLK OXL 46.1538
Pocket No.: 2; Query (leader) PDB : 5J32; Ligand: IPM; Similar sites found with APoc: 115
This union binding pocket(no: 2) in the query (biounit: 5j32.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2VWA PTY None
2 4Y9J UCC 0.992556
3 5OSW DIU 1.24069
4 3RGA ILD 1.41343
5 3ICS COA 1.48883
6 3ICT COA 1.48883
7 2QZO KN1 1.55039
8 5AAV GW5 1.5873
9 1TLL NAP 1.73697
10 4GV4 MEJ 1.96078
11 5MWY YNU 1.96721
12 4J26 EST 2.08333
13 6CEP NAD 2.09581
14 2OBD 2OB 2.23325
15 2OBD PCW 2.23325
16 1GQG DCD 2.28571
17 4GCZ FMN 2.33766
18 2WTX VDO 2.48139
19 4JNE ATP 2.48139
20 3D78 NBB 2.52101
21 5D9O BGC BGC BGC BGC 2.54958
22 3GWT 066 2.54958
23 1GV0 NAD 2.58065
24 5BNW 12V 2.72953
25 4GYW UDP 2.72953
26 3E2M E2M 2.97767
27 5CFT APC 3.24324
28 4QJR PIZ 3.26531
29 1ZDT PEF 3.3195
30 3DR4 G4M 3.32481
31 2PV7 NAD 3.3557
32 6ESN BWE 3.37079
33 1ZEM NAD 3.43511
34 4B9Q ATP 3.47395
35 1YYE 196 3.73134
36 2X5W K2B 3.86364
37 5IUW IAC 3.97022
38 2V1O COA 3.97351
39 4NKW PLO 4.04858
40 1A8R GTP 4.0724
41 5VC5 96M 4.15225
42 1GUZ NAD 4.19355
43 5QIN J2V 4.43038
44 4QOM PYG 4.4665
45 3VSV XYP 4.4665
46 1FDQ HXA 4.58015
47 5EY0 GTP 4.74453
48 1PZO CBT 4.94297
49 3U3U EAH 4.96278
50 4ZVV NAD 5.12048
51 4ZVV GN0 5.12048
52 3FP0 FP0 5.21092
53 2WD7 NAP 5.22388
54 6DQU GLY ILE ILE ASN THR LEU 5.45906
55 4U82 FPS 5.46875
56 1TMM APC 5.6962
57 1TMM HHR 5.6962
58 4KXL 6C6 5.92105
59 3VVY ET 6.18557
60 6BA2 7KM 6.44068
61 3CV9 VDX 6.45161
62 1EZ4 NAD 6.60377
63 5HSA FAS 6.69975
64 4V1F BQ1 6.97674
65 3OKI OKI 7.29614
66 5LPA 71R 7.40741
67 5LPA ATP 7.40741
68 6A5Y 9CR 7.45614
69 5XFV FMN 7.48503
70 2B4Q NAP 7.6087
71 2NPA MMB 7.77778
72 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 7.80142
73 2HFP NSI 7.80142
74 4BH1 SIA GAL NAG 7.83133
75 3EM0 CHD 7.97101
76 1FM9 570 8.08823
77 3H0A D30 8.08823
78 4DM8 REA 8.2397
79 1N1G BCP 8.46994
80 5WPJ NDP 8.68486
81 4YEE 4CQ 8.88889
82 5JCJ NAP 10.4167
83 4CLR NAP 10.4167
84 4CME NAP 10.4167
85 3BMQ NAP 10.4167
86 5JDC NAP 10.4167
87 3JQ9 NAP 10.4167
88 5K6A NAP 10.4167
89 3JQF NAP 10.4167
90 3JQ8 NAP 10.4167
91 4CM9 NAP 10.4167
92 5JDI NAP 10.4167
93 3BMO NAP 10.4167
94 4CMI NAP 10.4167
95 4CM8 NAP 10.4167
96 3JQ7 NAP 10.4167
97 3JQA NAP 10.4167
98 3JQB NAP 10.4167
99 3JQG NAP 10.4167
100 4CM4 NAP 10.4167
101 3BMN NAP 10.4167
102 4C01 QY9 10.9929
103 2WSB NAD 11.0236
104 3ND6 ATP 11.1111
105 1LEK GLU GLN TYR LYS PHE TYR SER VAL 11.3139
106 1JGS SAL 11.5942
107 5UWA 8ND 12.3153
108 1Z0N BCD 12.5
109 5F1R 42O 13.5021
110 5ZZ6 NAD 13.9423
111 5EXE 5SR 15.5556
112 3RV5 DXC 15.7303
113 6GG9 FMN 16.0494
114 4NG2 OHN 19.469
115 5ZCO PEK 21.2766
Pocket No.: 3; Query (leader) PDB : 5J32; Ligand: IPM; Similar sites found with APoc: 27
This union binding pocket(no: 3) in the query (biounit: 5j32.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5DX3 EST 1.53257
2 5WGQ EST 1.53257
3 5HYR EST 1.55039
4 4MGB XDH 1.56863
5 3UUD EST 1.59363
6 4J24 EST 2.08333
7 3OLL EST 2.08333
8 3CY2 MB9 2.2293
9 4IRX INS 2.7027
10 2WMC MGP 2.80899
11 1RRM APR 2.84974
12 4BFW ZVW 3.14465
13 5EYK 5U5 3.62319
14 3TKY SAH 3.80435
15 6F68 GSH 4.06504
16 6F68 4EU 4.06504
17 3FRQ ERY 4.10256
18 2WCJ M21 4.96454
19 6CHP F0Y 4.96894
20 1ZGA HMK 6.44258
21 5XWV 8H6 7.69231
22 1GTE FMN 8.43672
23 1GTE IUR 8.43672
24 6D6L FY4 9.41177
25 4B6C B5U 11.7347
26 3QDJ ALA ALA GLY ILE GLY ILE LEU THR VAL 12
27 1MID LAP 14.2857
Pocket No.: 4; Query (leader) PDB : 5J32; Ligand: IPM; Similar sites found with APoc: 12
This union binding pocket(no: 4) in the query (biounit: 5j32.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2OBF SAH 2.42215
2 3G5D 1N1 2.44755
3 2HU5 GLY PHE 2.48139
4 2VL8 UDP 2.72953
5 3F3E LEU 5.21092
6 5A65 TPP 5.52995
7 4G86 BNT 5.98592
8 2ZCQ B65 6.48464
9 5YBN AKG 6.6879
10 4O1Z MXM 6.69975
11 4ITR GDP 7.32984
12 2I7C AAT 8.12721
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