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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
Ligand no: 1; Ligand: MC4; Similar ligands found: 138
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 CAA 0.825758 0.934783
12 COK 0.823077 0.904255
13 3HC 0.818182 0.934783
14 MLC 0.818182 0.924731
15 IVC 0.818182 0.934783
16 1HE 0.818182 0.905263
17 BCO 0.818182 0.924731
18 CMC 0.816794 0.904255
19 FYN 0.815385 0.923913
20 30N 0.8125 0.85
21 COO 0.81203 0.945652
22 MCA 0.81203 0.935484
23 SCA 0.80597 0.924731
24 0T1 0.80315 0.903226
25 COA 0.80315 0.923913
26 DCA 0.801587 0.903226
27 HXC 0.801471 0.925532
28 HGG 0.8 0.924731
29 COW 0.8 0.914894
30 BYC 0.8 0.924731
31 1GZ 0.8 0.935484
32 IRC 0.8 0.934783
33 FAQ 0.794118 0.924731
34 BCA 0.794118 0.914894
35 A1S 0.791045 0.904255
36 2NE 0.789855 0.905263
37 GRA 0.788321 0.924731
38 ETB 0.787402 0.87234
39 COF 0.786765 0.885417
40 AMX 0.784615 0.913043
41 TGC 0.782609 0.914894
42 2CP 0.779412 0.914894
43 CMX 0.778626 0.903226
44 SCO 0.778626 0.903226
45 1CZ 0.776978 0.914894
46 CO8 0.776978 0.925532
47 2KQ 0.773723 0.925532
48 3CP 0.773723 0.904255
49 CS8 0.77305 0.915789
50 FAM 0.772727 0.884211
51 FCX 0.772727 0.875
52 ST9 0.771429 0.925532
53 MFK 0.771429 0.925532
54 UCC 0.771429 0.925532
55 5F9 0.771429 0.925532
56 MYA 0.771429 0.925532
57 DCC 0.771429 0.925532
58 SCD 0.77037 0.903226
59 4CA 0.768116 0.894737
60 HAX 0.766917 0.884211
61 NMX 0.762963 0.858586
62 WCA 0.760563 0.925532
63 0FQ 0.758865 0.904255
64 4CO 0.758865 0.894737
65 CA6 0.755556 0.843137
66 MCD 0.755556 0.904255
67 NHW 0.755245 0.905263
68 4KX 0.755245 0.956989
69 HDC 0.755245 0.925532
70 UOQ 0.755245 0.905263
71 NHM 0.755245 0.905263
72 01A 0.753521 0.867347
73 CIC 0.751773 0.904255
74 MRR 0.75 0.925532
75 MRS 0.75 0.925532
76 HFQ 0.75 0.885417
77 DAK 0.744828 0.915789
78 YNC 0.744828 0.935484
79 CAJ 0.744526 0.904255
80 0ET 0.741259 0.905263
81 8Z2 0.739726 0.93617
82 1CV 0.736111 0.924731
83 YE1 0.733813 0.893617
84 1HA 0.731544 0.905263
85 01K 0.726667 0.924731
86 7L1 0.725926 0.935484
87 CA8 0.723404 0.843137
88 NHQ 0.718121 0.913979
89 CCQ 0.715278 0.926316
90 F8G 0.710526 0.947368
91 COT 0.710526 0.904255
92 S0N 0.703448 0.884211
93 CA3 0.690323 0.904255
94 CA5 0.679245 0.867347
95 UCA 0.675 0.925532
96 CO7 0.673611 0.945652
97 93P 0.664596 0.894737
98 93M 0.654545 0.894737
99 COD 0.651852 0.913043
100 4BN 0.626437 0.947368
101 5TW 0.626437 0.947368
102 OXT 0.614943 0.907216
103 HMG 0.614379 0.913979
104 PLM COA 0.596154 0.914894
105 COA PLM 0.596154 0.914894
106 JBT 0.582418 0.87
107 BSJ 0.567416 0.876289
108 ASP ASP ASP ILE CMC NH2 0.558824 0.884211
109 PAP 0.552846 0.75
110 ACE SER ASP ALY THR NH2 COA 0.521739 0.904255
111 191 0.50625 0.918367
112 SFC 0.505952 0.946237
113 RFC 0.505952 0.946237
114 PPS 0.503876 0.7
115 A3P 0.491935 0.73913
116 0WD 0.486667 0.787234
117 PTJ 0.43662 0.806452
118 3AM 0.432 0.728261
119 PAJ 0.428571 0.817204
120 3OD 0.426573 0.763441
121 ATR 0.425373 0.73913
122 PUA 0.425 0.778947
123 A22 0.42446 0.752688
124 ADP 0.419847 0.76087
125 A2D 0.418605 0.741935
126 AGS 0.414815 0.765957
127 SAP 0.414815 0.765957
128 OAD 0.412587 0.763441
129 48N 0.407895 0.768421
130 2A5 0.407407 0.782609
131 A2R 0.407143 0.752688
132 9X8 0.402778 0.765957
133 NA7 0.402778 0.793478
134 A A A 0.402778 0.771739
135 BA3 0.401515 0.741935
136 YLB 0.4 0.840426
137 HEJ 0.4 0.76087
138 ATP 0.4 0.76087
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: 40
This union binding pocket(no: 1) in the query (biounit: 2gce.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 2Q3M MLA 1.22699
2 4A59 AMP 1.66667
3 5Z3I ADE 1.88679
4 1RJW ETF 2.35988
5 5OCQ CIT 2.45614
6 2QES ADE 2.68199
7 4D8N 0HM 3.13901
8 5TCI MLI 3.26087
9 1TZD ADP 3.27273
10 1VMK GUN 3.61011
11 5FUS DAO 3.83275
12 2F5X ASP 3.84615
13 1RYH GNP 4.4335
14 2WMO GTP 4.44444
15 3GFS FMN 4.5977
16 4Q0A 4OA 4.63576
17 5OSW AE4 4.72222
18 3UVD MB3 4.83871
19 1Y7P RIP 4.93274
20 3RKR NAP 5.34351
21 1CEB AMH 5.68182
22 5LWY OLB 5.82192
23 1QH8 HCA 6.11111
24 1YXM ADE 6.27063
25 3KO0 TFP 6.93069
26 5UGW GSH 7.42857
27 5X80 SAL 7.5
28 2UYQ SAM 8.70968
29 2P8O BVA 12.2137
30 1DKU AP2 12.6183
31 5XNA SHV 13.0435
32 3QPB URA 15.9574
33 5C1M OLC 27.2
34 1Q7E MET 27.5
35 1VGR COA 28.3333
36 2VJM COA 28.6111
37 3UBM COA 34.8684
38 1XVV CCQ 39.1667
39 1XA4 COA 40.8333
40 5E8J SAH 40.9091
Pocket No.: 2; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found with APoc: 36
This union binding pocket(no: 2) in the query (biounit: 2gce.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZJS 4P0 0.869565
2 4A59 AMP 1.66667
3 5OCQ CIT 2.45614
4 1A5Z FBP 2.50784
5 1VR0 3SL 2.83401
6 6EL3 NAP 3.05556
7 1HPG BOC ALA ALA PRO GLU 3.20856
8 5TCI MLI 3.26087
9 1WD4 AHR 3.33333
10 1VMK GUN 3.61011
11 1W6U NAP 3.64238
12 5YSI NCA 3.94737
13 1O9P MLA 4.16667
14 2IMP LAC 4.16667
15 1ZEM NAD 4.58015
16 3W9F I3P 4.61538
17 1KYZ SAH 4.72222
18 3RKR NAP 5.34351
19 6BSM E7D 5.47264
20 1KQR MNA 5.58659
21 1CEB AMH 5.68182
22 4G86 BNT 5.98592
23 1YXM ADE 6.27063
24 4DDY DN6 6.84411
25 3KO0 TFP 6.93069
26 4V0K GDP 7.10059
27 5X80 SAL 7.5
28 1DKU AP2 12.6183
29 3QPB URA 15.9574
30 3K1X DBX 26.1538
31 1Q7E MET 27.5
32 1VGR COA 28.3333
33 2VJM COA 28.6111
34 3UBM COA 34.8684
35 1XVV CCQ 39.1667
36 1XA4 COA 40.8333
Pocket No.: 3; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found with APoc: 19
This union binding pocket(no: 3) in the query (biounit: 2gce.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZJS 4P0 0.869565
2 1A5Z FBP 2.50784
3 1VR0 3SL 2.83401
4 6EL3 NAP 3.05556
5 1HPG BOC ALA ALA PRO GLU 3.20856
6 1WD4 AHR 3.33333
7 1W6U NAP 3.64238
8 5YSI NCA 3.94737
9 1O9P MLA 4.16667
10 2IMP LAC 4.16667
11 1ZEM NAD 4.58015
12 3W9F I3P 4.61538
13 1KYZ SAH 4.72222
14 6BSM E7D 5.47264
15 1KQR MNA 5.58659
16 4G86 BNT 5.98592
17 4DDY DN6 6.84411
18 4V0K GDP 7.10059
19 3K1X DBX 26.1538
Pocket No.: 4; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found with APoc: 8
This union binding pocket(no: 4) in the query (biounit: 2gce.bio2) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 5Z3I ADE 1.88679
2 1RJW ETF 2.35988
3 2AWN ADP 3.33333
4 5Y02 HBX 3.73832
5 1QH8 HCA 6.11111
6 2EA1 GPG 6.53061
7 5XNA SHV 13.0435
8 4RJD TFP 15.1515
Pocket No.: 5; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 2gce.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 1SZ2 BGC 1.80723
2 4CS9 AMP 2.1164
3 3NNF AKG 6.39535
Pocket No.: 6; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found with APoc: 5
This union binding pocket(no: 6) in the query (biounit: 2gce.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4CS9 AMP 2.1164
2 3NNF AKG 6.39535
3 5Y3N 8MF 7.5
4 1ZOY UQ1 8.73786
5 5Z84 CHD 35.5932
Pocket No.: 7; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found with APoc: 2
This union binding pocket(no: 7) in the query (biounit: 2gce.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4RM0 FUC NDG GAL 3.16456
2 1CT9 GLN 6.38889
Pocket No.: 8; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found with APoc: 4
This union binding pocket(no: 8) in the query (biounit: 2gce.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 1H16 DTL 1.66667
2 2AWN ADP 3.33333
3 4D5B ACX 4.42478
4 1CT9 GLN 6.38889
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