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Receptor
PDB id Resolution Class Description Source Keywords
5bww 1.82 Å EC: 2.6.1.42 X-RAY CRYSTAL STRUCTURE AT 1.82A RESOLUTION OF HUMAN MITOCHO BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYA MIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR HOMO SAPIENS FOLD TYPE IV TRANSFERASE
Ref.: THE DISCOVERY OF IN VIVO ACTIVE MITOCHONDRIAL BRANC AMINOTRANSFERASE (BCATM) INHIBITORS BY HYBRIDIZING AND HTS HITS. J.MED.CHEM. V. 58 7140 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL B:411;
A:410;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
EDO B:408;
B:405;
A:407;
B:406;
A:406;
A:409;
A:403;
B:409;
A:404;
A:408;
A:405;
B:410;
B:407;
B:404;
Invalid;
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;
none;
submit data
62.068 C2 H6 O2 C(CO)...
PLP B:401;
A:401;
Invalid;
Invalid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
DMS B:403;
Invalid;
none;
submit data
78.133 C2 H6 O S CS(=O...
GOL A:411;
B:412;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
4W6 B:402;
A:402;
Valid;
Valid;
none;
none;
ic50 = 0.5 uM
313.354 C16 H19 N5 O2 CCCC1...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5I60 2.12 Å EC: 2.6.1.42 X-RAY CRYSTAL STRUCTURE AT 2.12A RESOLUTION OF HUMAN MITOCHO BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIC OMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR. HOMO SAPIENS FOLD TYPE IV TRANSFERASE
Ref.: STRUCTURALLY DIVERSE MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) LEADS WITH VARYING BINDING IDENTIFIED BY FRAGMENT SCREENING. J.MED.CHEM. V. 59 2452 2016
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5CR5 ic50 = 2 uM EL1 C24 H24 Br N3 O5 S2 CNC(=O)c1c....
2 1KT8 - ILP C14 H23 N2 O7 P CC[C@H](C)....
3 5BWR ic50 = 25 uM 4VT C14 H10 N4 O c1ccc(cc1)....
4 5I5W ic50 = 1 mM 68B C11 H9 N3 O c1ccc(cc1)....
5 5I5S - NVU C9 H7 N O3 c1ccc2c(c1....
6 5BWW ic50 = 0.5 uM 4W6 C16 H19 N5 O2 CCCC1=CC(=....
7 5I5U - 67Y C12 H15 N O2 c1ccc2c(c1....
8 5I5Y ic50 = 1 uM 68D C16 H13 N3 O4 S Cc1c2c(sc1....
9 5I60 ic50 = 0.00000001 M 67W C18 H15 N3 O3 c1ccc(c(c1....
10 5BWX ic50 = 16 nM 4W4 C18 H17 Cl F N5 O CCCCC1=CC(....
11 5I5V ic50 = 63 uM 68A C9 H8 N2 O3 S Cc1c2c(sc1....
12 5BWV ic50 = 79 nM 775 C17 H16 Cl N5 O CCCC1=CC(=....
13 5HNE ic50 = 50 nM EL2 C25 H24 Br N5 O2 S CNC(=O)c1c....
14 5BWU ic50 = 0.63 uM 4VR C15 H16 Br N5 O CCCC1=CC(=....
15 2HDK Kd = 6.1 mM COI C6 H10 O3 CC(C)CC(=O....
16 2A1H Ki = 65.4 mM GBN C9 H17 N O2 C1CCC(CC1)....
17 5I5T - 67X C10 H14 N2 O2 S C[C@@H]1Cc....
18 5I5X ic50 = 0.2 uM 68C C10 H7 N5 O2 S2 Cc1c2c(sc1....
19 2HG8 - MLE C7 H15 N O2 CC(C)C[C@@....
20 1KTA - KIV C5 H8 O3 CC(C)C(=O)....
21 5BWT - 4VS C10 H10 N4 O CCC1=CC(=O....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5CR5 ic50 = 2 uM EL1 C24 H24 Br N3 O5 S2 CNC(=O)c1c....
2 1KT8 - ILP C14 H23 N2 O7 P CC[C@H](C)....
3 5BWR ic50 = 25 uM 4VT C14 H10 N4 O c1ccc(cc1)....
4 5I5W ic50 = 1 mM 68B C11 H9 N3 O c1ccc(cc1)....
5 5I5S - NVU C9 H7 N O3 c1ccc2c(c1....
6 5BWW ic50 = 0.5 uM 4W6 C16 H19 N5 O2 CCCC1=CC(=....
7 5I5U - 67Y C12 H15 N O2 c1ccc2c(c1....
8 5I5Y ic50 = 1 uM 68D C16 H13 N3 O4 S Cc1c2c(sc1....
9 5I60 ic50 = 0.00000001 M 67W C18 H15 N3 O3 c1ccc(c(c1....
10 5BWX ic50 = 16 nM 4W4 C18 H17 Cl F N5 O CCCCC1=CC(....
11 5I5V ic50 = 63 uM 68A C9 H8 N2 O3 S Cc1c2c(sc1....
12 5BWV ic50 = 79 nM 775 C17 H16 Cl N5 O CCCC1=CC(=....
13 5HNE ic50 = 50 nM EL2 C25 H24 Br N5 O2 S CNC(=O)c1c....
14 5BWU ic50 = 0.63 uM 4VR C15 H16 Br N5 O CCCC1=CC(=....
15 2HDK Kd = 6.1 mM COI C6 H10 O3 CC(C)CC(=O....
16 2A1H Ki = 65.4 mM GBN C9 H17 N O2 C1CCC(CC1)....
17 5I5T - 67X C10 H14 N2 O2 S C[C@@H]1Cc....
18 5I5X ic50 = 0.2 uM 68C C10 H7 N5 O2 S2 Cc1c2c(sc1....
19 2HG8 - MLE C7 H15 N O2 CC(C)C[C@@....
20 1KTA - KIV C5 H8 O3 CC(C)C(=O)....
21 5BWT - 4VS C10 H10 N4 O CCC1=CC(=O....
22 2COI Ki = 3.5 mM GBN C9 H17 N O2 C1CCC(CC1)....
23 2COJ Ki = 1.3 mM GBN C9 H17 N O2 C1CCC(CC1)....
24 2COG - 4MV C6 H12 O2 CC(C)CCC(=....
25 2ABJ ic50 = 0.8 uM CBC C16 H10 Cl F3 N2 O4 S c1ccc(c(c1....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5CR5 ic50 = 2 uM EL1 C24 H24 Br N3 O5 S2 CNC(=O)c1c....
2 1KT8 - ILP C14 H23 N2 O7 P CC[C@H](C)....
3 5BWR ic50 = 25 uM 4VT C14 H10 N4 O c1ccc(cc1)....
4 5I5W ic50 = 1 mM 68B C11 H9 N3 O c1ccc(cc1)....
5 5I5S - NVU C9 H7 N O3 c1ccc2c(c1....
6 5BWW ic50 = 0.5 uM 4W6 C16 H19 N5 O2 CCCC1=CC(=....
7 5I5U - 67Y C12 H15 N O2 c1ccc2c(c1....
8 5I5Y ic50 = 1 uM 68D C16 H13 N3 O4 S Cc1c2c(sc1....
9 5I60 ic50 = 0.00000001 M 67W C18 H15 N3 O3 c1ccc(c(c1....
10 5BWX ic50 = 16 nM 4W4 C18 H17 Cl F N5 O CCCCC1=CC(....
11 5I5V ic50 = 63 uM 68A C9 H8 N2 O3 S Cc1c2c(sc1....
12 5BWV ic50 = 79 nM 775 C17 H16 Cl N5 O CCCC1=CC(=....
13 5HNE ic50 = 50 nM EL2 C25 H24 Br N5 O2 S CNC(=O)c1c....
14 5BWU ic50 = 0.63 uM 4VR C15 H16 Br N5 O CCCC1=CC(=....
15 2HDK Kd = 6.1 mM COI C6 H10 O3 CC(C)CC(=O....
16 2A1H Ki = 65.4 mM GBN C9 H17 N O2 C1CCC(CC1)....
17 5I5T - 67X C10 H14 N2 O2 S C[C@@H]1Cc....
18 5I5X ic50 = 0.2 uM 68C C10 H7 N5 O2 S2 Cc1c2c(sc1....
19 2HG8 - MLE C7 H15 N O2 CC(C)C[C@@....
20 1KTA - KIV C5 H8 O3 CC(C)C(=O)....
21 5BWT - 4VS C10 H10 N4 O CCC1=CC(=O....
22 2COI Ki = 3.5 mM GBN C9 H17 N O2 C1CCC(CC1)....
23 2COJ Ki = 1.3 mM GBN C9 H17 N O2 C1CCC(CC1)....
24 2COG - 4MV C6 H12 O2 CC(C)CCC(=....
25 2ABJ ic50 = 0.8 uM CBC C16 H10 Cl F3 N2 O4 S c1ccc(c(c1....
26 3UZO - PLP C8 H10 N O6 P Cc1c(c(c(c....
27 3UYY - PLP C8 H10 N O6 P Cc1c(c(c(c....
28 3HT5 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
29 5U3F - 7TS C11 H14 N3 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4W6; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 4W6 1 1
2 775 0.404255 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5I60; Ligand: 67W; Similar sites found with APoc: 110
This union binding pocket(no: 1) in the query (biounit: 5i60.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 3R4S SIA 1.35501
2 4GPS CIT 1.35501
3 5KJW 53C 1.62602
4 4XFR CIT 1.89702
5 4XG0 CIT 1.89702
6 4F2Q QUS 1.93798
7 4YJK URA 1.98413
8 2PEL LBT 2.11864
9 3ZO7 K6H 2.12766
10 2B6N ALA PRO THR 2.15827
11 3K5I AIR 2.16802
12 1C3X 8IG 2.43902
13 3AWJ COA 2.43902
14 5M6N 7H9 2.54237
15 4HNN LYS 2.60116
16 6CZI 38E 2.67857
17 1T9D P22 2.71003
18 1J78 OLA 2.71003
19 3SIX GDP 2.72727
20 1NW4 IMH 2.89855
21 1TL2 NDG 2.9661
22 2ZBA COA 2.98103
23 5NM7 GLY 3.00752
24 5ZI9 FLC 3.07692
25 1NE7 AGP 3.11419
26 4URF 1PS 3.22581
27 2OEM 1AE 3.25203
28 5FPE 3TR 3.25203
29 1TKU 5RP 3.43137
30 3GFS FMN 3.44828
31 3B8I OXL 3.48432
32 4KFU ACP 3.77358
33 1Q19 SSC 3.79404
34 2BO4 FLC 3.79404
35 3O3U MLR 3.79404
36 1T3D CYS 3.80623
37 2J5V PCA 3.81471
38 2G30 ALA ALA PHE 3.87597
39 2WPB ZZI 3.94737
40 1OGZ EQU 4
41 5LI9 ACP 4
42 2W5P CL8 4.02685
43 1P7T PYR 4.06504
44 2VWT PYR 4.11985
45 5C2N NAG 4.16667
46 3NOJ PYR 4.20168
47 3EUF BAU 4.26829
48 5XK9 GST 4.31034
49 3UW4 MAA CHG PRO 0DQ 4.34783
50 6BR8 6OU 4.36508
51 5TBS ADE 4.52962
52 6BU0 IHP 4.58015
53 4ZWP M44 4.60705
54 1JE1 GMP 4.66102
55 4B5W PYR 4.6875
56 3KIF GDL 4.71698
57 3CF6 SP1 4.79042
58 6G1P CIT 4.85714
59 4I6H 1C8 4.87013
60 5CLO NS8 5.08475
61 1LSH PLD 5.42005
62 1NXJ TLA 5.46448
63 2HK9 ATR 5.81818
64 5LWY OLB 5.88235
65 2DC1 CIT 5.9322
66 6BHV DQV 5.96206
67 4WJT NAG 5.98802
68 3CM2 X23 6.15385
69 3KIH GDL 6.18557
70 5OQW A4E 6.29921
71 1Z34 2FD 6.38298
72 1H74 ILE 6.41892
73 2D3M COA 6.50407
74 4IF4 BEF 6.73077
75 1LK7 DER 6.9869
76 5C83 4YN 7.27273
77 6F4W FMC 7.29614
78 2NU5 NAG 7.37705
79 2HYQ MAN MAN 7.37705
80 2NUO BGC 7.37705
81 2GUC MAN 7.37705
82 2GUD MAN 7.37705
83 2HYR BGC GLC 7.37705
84 5YZC NAG 7.44681
85 3GLC R5P 7.45763
86 5A96 GTP 7.63052
87 1ODJ GMP 8.08511
88 5K3W PLP 8.30671
89 2CDU ADP 8.40108
90 3IX9 MTX 8.42105
91 3LGS ADE 8.61423
92 3AB4 THR 8.98876
93 4ZEV M6P 9.45946
94 4PIV 2W4 9.4851
95 1VHW ADN 9.88142
96 3KCC CMP 10.3846
97 1TUK PGM 10.4478
98 3LST SAH 10.6322
99 5E5U MLI 11.5578
100 4ZJS 4P0 11.7391
101 4MTI 2DX 13.0435
102 1I2L DCS 13.7546
103 3QPB URA 14.1844
104 3QPB R1P 14.1844
105 6FA4 D1W 14.4509
106 3UW5 MAA CHG PRO 0DQ 14.6552
107 5U9J GER 16.568
108 3KO0 TFP 16.8317
109 5F6U 5VK 17.1975
110 3DAA PDD 20.5776
Pocket No.: 2; Query (leader) PDB : 5I60; Ligand: 67W; Similar sites found with APoc: 54
This union binding pocket(no: 2) in the query (biounit: 5i60.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 5YSI NCA None
2 2Z48 A2G 1.62602
3 1SKQ GDP 1.62602
4 1G2O IMH 1.86567
5 4XDA ADP 1.94175
6 1FDJ 13P 2.20386
7 2H92 C5P 2.28311
8 6MDE MEV 2.31023
9 5M4Q PRO 2.43902
10 3DJF BC3 2.43902
11 4O48 ASP 3.01205
12 1ZOS MTM 3.04348
13 2ZL4 ALA ALA ALA ALA 3.06122
14 3JQ9 AX1 3.125
15 3BJE R1P 3.15186
16 1IHU ADP 3.52304
17 4JJJ CBK 3.52304
18 3ITJ CIT 3.5503
19 3C4M MAL 3.79404
20 5IQZ MAL 3.79404
21 2XOC ADP 3.83142
22 5BSH PRO 3.97112
23 1VMK GUN 4.06504
24 4UWM FMN 4.06504
25 3EXS 5RP 4.0724
26 3ZZH NLG 4.23453
27 5J6Y GLC 4.25532
28 5J6Y BGC 4.25532
29 6D1U MAL 4.33604
30 3GUZ PAF 4.54545
31 4JUI EGR 4.60705
32 2WN6 NDP 4.60705
33 4FBL SPD 4.62633
34 4ZNO SUC 4.77612
35 1NMU MTT 4.80769
36 4O08 PO6 4.87805
37 4ZUL UN1 5.69106
38 5OJL TXP 6.04027
39 5IFK HPA 6.08974
40 2ZSC BTN 6.38298
41 5CQG 55C 6.50407
42 1NT4 G1P 6.50407
43 3JUC PCA 6.53595
44 4L9Z OXL 6.78466
45 3RDV ASP SER TRP LYS ASP GLY CYS TYR 6.94444
46 3VYK MMA MAN NAG MAN NAG NAG 6.97674
47 5XLX SAH 7.0922
48 4M1U A2G MBG 7.14286
49 4EKQ NPO 7.48663
50 1DKF OLA 8.15451
51 5KK4 44E 8.33333
52 1APZ ASP 9.92908
53 4IS0 1R4 9.95851
54 4JGX PLM 13.9535
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