Receptor
PDB id Resolution Class Description Source Keywords
2YIM 1.41 Å EC: 5.1.99.4 THE ENOLISATION CHEMISTRY OF A THIOESTER-DEPENDENT RACEMASE: THE 1.4 A CRYSTAL STRUCTURE OF A COMPLEX WITH A P LANAR REACTION INTERMEDIATE ANALOGUE MYCOBACTERIUM TUBERCULOSIS ISOMERASE METHYL-COA RACEMASE TRANSITION STATE MOLECULAR DYNAMICS QM/MM OXYANION HOLE
Ref.: THE ENOLIZATION CHEMISTRY OF A THIOESTER-DEPENDENT RACEMASE: THE 1.4 A CRYSTAL STRUCTURE OF A REACTION INTERMEDIATE COMPLEX CHARACTERIZED BY DETAILED QM/M CALCULATIONS. J PHYS CHEM B V. 116 3619 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1361;
B:1362;
C:1361;
C:1362;
D:1362;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MC4 A:1363;
B:1363;
C:1363;
D:1363;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Kd = 120 uM
864.626 C26 H41 N7 O18 P3 S C/C(=...
PO4 B:1361;
D:1361;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GCE 1.85 Å EC: 5.1.99.4 THE 1,1-PROTON TRANSFER REACTION MECHANISM BY ALPHA-METHYLAC RACEMASE IS CATALYZED BY AN ASPARTATE/HISTIDINE PAIR AND INS MOOTH, METHIONINE-RICH SURFACE FOR BINDING THE FATTY ACYL MYCOBACTERIUM TUBERCULOSIS ALPHA-METHYLACYL-COA RACEMASE RACEMASE COA TRANSFERASE PRTRANSFER COENZYME A ISOMERASE
Ref.: THE CATALYSIS OF THE 1,1-PROTON TRANSFER BY ALPHA-METHYL-ACYL-COA RACEMASE IS COUPLED TO A MOVE THE FATTY ACYL MOIETY OVER A HYDROPHOBIC, METHIONIN SURFACE J.MOL.BIOL. V. 367 1145 2007
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YIM Kd = 120 uM MC4 C26 H41 N7 O18 P3 S C/C(=C([O-....
2 2GD6 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2GCI - MRR C36 H64 N7 O17 P3 S CCCCCCCCCC....
4 2GD0 - MRS C36 H64 N7 O17 P3 S CCCCCCCCCC....
5 2GD2 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 2GCE Kd = 24.5 uM RFC C34 H53 N7 O17 P3 S CC(C)Cc1cc....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YIM Kd = 120 uM MC4 C26 H41 N7 O18 P3 S C/C(=C([O-....
2 2GD6 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2GCI - MRR C36 H64 N7 O17 P3 S CCCCCCCCCC....
4 2GD0 - MRS C36 H64 N7 O17 P3 S CCCCCCCCCC....
5 2GD2 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 2GCE Kd = 24.5 uM RFC C34 H53 N7 O17 P3 S CC(C)Cc1cc....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YIM Kd = 120 uM MC4 C26 H41 N7 O18 P3 S C/C(=C([O-....
2 2GD6 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2GCI - MRR C36 H64 N7 O17 P3 S CCCCCCCCCC....
4 2GD0 - MRS C36 H64 N7 O17 P3 S CCCCCCCCCC....
5 2GD2 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 2GCE Kd = 24.5 uM RFC C34 H53 N7 O17 P3 S CC(C)Cc1cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MC4; Similar ligands found: 162
No: Ligand ECFP6 Tc MDL keys Tc
1 MC4 1 1
2 ACO 0.887097 0.935484
3 3KK 0.84375 0.945652
4 COS 0.84127 0.904255
5 CAO 0.84127 0.894737
6 2MC 0.838462 0.967742
7 OXK 0.837209 0.924731
8 SOP 0.837209 0.924731
9 CO6 0.830769 0.945652
10 1VU 0.830769 0.935484
11 KFV 0.827068 0.888889
12 CAA 0.825758 0.934783
13 COK 0.823077 0.904255
14 1HE 0.818182 0.905263
15 IVC 0.818182 0.934783
16 3HC 0.818182 0.934783
17 MLC 0.818182 0.924731
18 BCO 0.818182 0.924731
19 CMC 0.816794 0.904255
20 FYN 0.815385 0.923913
21 30N 0.8125 0.85
22 COO 0.81203 0.945652
23 MCA 0.81203 0.935484
24 SCA 0.80597 0.924731
25 YXS 0.80597 0.861386
26 YXR 0.80597 0.861386
27 0T1 0.80315 0.903226
28 COA 0.80315 0.923913
29 DCA 0.801587 0.903226
30 HXC 0.801471 0.925532
31 IRC 0.8 0.934783
32 BYC 0.8 0.924731
33 1GZ 0.8 0.935484
34 COW 0.8 0.914894
35 HGG 0.8 0.924731
36 BCA 0.794118 0.914894
37 FAQ 0.794118 0.924731
38 A1S 0.791045 0.904255
39 2NE 0.789855 0.905263
40 GRA 0.788321 0.924731
41 ETB 0.787402 0.87234
42 COF 0.786765 0.885417
43 AMX 0.784615 0.913043
44 TGC 0.782609 0.914894
45 2CP 0.779412 0.914894
46 SCO 0.778626 0.903226
47 CMX 0.778626 0.903226
48 1CZ 0.776978 0.914894
49 CO8 0.776978 0.925532
50 3CP 0.773723 0.904255
51 2KQ 0.773723 0.925532
52 CS8 0.77305 0.915789
53 FCX 0.772727 0.875
54 FAM 0.772727 0.884211
55 DCC 0.771429 0.925532
56 MYA 0.771429 0.925532
57 5F9 0.771429 0.925532
58 ST9 0.771429 0.925532
59 MFK 0.771429 0.925532
60 UCC 0.771429 0.925532
61 SCD 0.77037 0.903226
62 4CA 0.768116 0.894737
63 HAX 0.766917 0.884211
64 KGJ 0.764706 0.868687
65 NMX 0.762963 0.858586
66 WCA 0.760563 0.925532
67 4CO 0.758865 0.894737
68 0FQ 0.758865 0.904255
69 J5H 0.756944 0.924731
70 CA6 0.755556 0.843137
71 KGP 0.755556 0.861386
72 YZS 0.755556 0.861386
73 MCD 0.755556 0.904255
74 4KX 0.755245 0.956989
75 HDC 0.755245 0.925532
76 NHW 0.755245 0.905263
77 NHM 0.755245 0.905263
78 UOQ 0.755245 0.905263
79 01A 0.753521 0.867347
80 CIC 0.751773 0.904255
81 HFQ 0.75 0.885417
82 MRR 0.75 0.925532
83 MRS 0.75 0.925532
84 KGA 0.748201 0.86
85 DAK 0.744828 0.915789
86 YNC 0.744828 0.935484
87 CAJ 0.744526 0.904255
88 0ET 0.741259 0.905263
89 8Z2 0.739726 0.93617
90 1CV 0.736111 0.924731
91 LCV 0.733813 0.852941
92 SO5 0.733813 0.852941
93 YE1 0.733813 0.893617
94 1HA 0.731544 0.905263
95 01K 0.726667 0.924731
96 7L1 0.725926 0.935484
97 CA8 0.723404 0.843137
98 NHQ 0.718121 0.913979
99 CCQ 0.715278 0.926316
100 F8G 0.710526 0.947368
101 COT 0.710526 0.904255
102 S0N 0.703448 0.884211
103 CA3 0.690323 0.904255
104 CA5 0.679245 0.867347
105 UCA 0.675 0.925532
106 CO7 0.673611 0.945652
107 93P 0.664596 0.894737
108 RMW 0.658385 0.925532
109 93M 0.654545 0.894737
110 COD 0.651852 0.913043
111 N9V 0.635762 0.894737
112 BUA COA 0.628378 0.913979
113 4BN 0.626437 0.947368
114 5TW 0.626437 0.947368
115 6NA COA 0.618421 0.914894
116 OXT 0.614943 0.907216
117 HMG 0.614379 0.913979
118 COA FLC 0.608392 0.913043
119 MYR COA 0.596154 0.914894
120 PLM COA 0.596154 0.914894
121 DKA COA 0.596154 0.914894
122 X90 COA 0.596154 0.914894
123 DCR COA 0.596154 0.914894
124 EO3 COA 0.596154 0.914894
125 DAO COA 0.596154 0.914894
126 JBT 0.582418 0.87
127 BSJ 0.567416 0.876289
128 ASP ASP ASP ILE NH2 CMC 0.558824 0.884211
129 PAP 0.552846 0.75
130 ACE SER ASP ALY THR NH2 COA 0.521739 0.904255
131 SFC 0.505952 0.946237
132 RFC 0.505952 0.946237
133 PPS 0.503876 0.7
134 MET VAL ASN ALA CMC 0.494624 0.884211
135 A3P 0.491935 0.73913
136 0WD 0.486667 0.787234
137 5AD NJS 0.482955 0.946809
138 ACE MET LEU GLY PRO NH2 COA 0.462312 0.884211
139 PTJ 0.43662 0.806452
140 3AM 0.432 0.728261
141 PAJ 0.428571 0.817204
142 3OD 0.426573 0.763441
143 ATR 0.425373 0.73913
144 PUA 0.425 0.778947
145 A22 0.42446 0.752688
146 ADP 0.419847 0.76087
147 A2D 0.418605 0.741935
148 HQG 0.417266 0.752688
149 AGS 0.414815 0.765957
150 UBG 0.414773 0.783505
151 9BG 0.414013 0.731959
152 OAD 0.412587 0.763441
153 48N 0.407895 0.768421
154 2A5 0.407407 0.782609
155 A2R 0.407143 0.752688
156 8LE 0.405797 0.784946
157 NA7 0.402778 0.793478
158 9X8 0.402778 0.765957
159 BA3 0.401515 0.741935
160 HEJ 0.4 0.76087
161 YLB 0.4 0.840426
162 ATP 0.4 0.76087
Similar Ligands (3D)
Ligand no: 1; Ligand: MC4; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GCE; Ligand: SFC; 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: 2gce.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2GCE; Ligand: RFC; 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: 2gce.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2gce.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2GCE; Ligand: RFC; 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: 2gce.bio2) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2gce.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2GCE; Ligand: SFC; 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: 2gce.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2gce.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2GCE; Ligand: SFC; 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: 2gce.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
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