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Receptor
PDB id Resolution Class Description Source Keywords
6REQ 2.2 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE, 3-CARBOXYPROPYL-COA INHIBITOR COMP PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF SUBSTRATE COMPLEXES OF METHYLMALONYL-COA MUTASE. BIOCHEMISTRY V. 38 7999 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3CP A:1801;
C:2801;
Valid;
Valid;
none;
none;
submit data
853.623 C25 H42 N7 O18 P3 S CC(C)...
B12 A:1800;
C:2800;
Part of Protein;
Part of Protein;
none;
none;
submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
GOL A:3001;
C:3002;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1REQ 2 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: HOW COENZYME B12 RADICALS ARE GENERATED: THE CRYSTA STRUCTURE OF METHYLMALONYL-COENZYME A MUTASE AT 2 A RESOLUTION. STRUCTURE V. 4 339 1996
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3CP; Similar ligands found: 135
No: Ligand ECFP6 Tc MDL keys Tc
1 3CP 1 1
2 CMC 0.867188 1
3 A1S 0.853846 0.977273
4 SOP 0.844961 0.977273
5 CMX 0.84252 0.977012
6 CIC 0.837037 1
7 CAO 0.834646 0.944444
8 COS 0.834646 0.955056
9 SCO 0.828125 0.977012
10 2CP 0.827068 0.988636
11 GRA 0.822222 0.977273
12 ACO 0.821705 0.944444
13 OXK 0.816794 0.977273
14 SCA 0.813433 0.977273
15 MLC 0.81203 0.977273
16 FYN 0.80916 0.977012
17 3KK 0.80916 0.955056
18 COF 0.807407 0.955556
19 AMX 0.806202 0.965517
20 COO 0.80597 0.955056
21 SCD 0.804511 0.977012
22 COK 0.80303 0.955056
23 4CA 0.801471 0.966292
24 1VU 0.796992 0.944444
25 CO6 0.796992 0.955056
26 0T1 0.796875 0.954545
27 COA 0.796875 0.977012
28 DCA 0.795276 0.932584
29 HGG 0.794118 0.977273
30 2KQ 0.794118 0.955556
31 MCA 0.792593 0.966292
32 30N 0.792308 0.894737
33 2MC 0.791045 0.913979
34 TGC 0.789855 0.988636
35 MCD 0.789474 0.955056
36 0ET 0.785714 0.955556
37 BCO 0.785185 0.955056
38 3HC 0.785185 0.965909
39 IVC 0.785185 0.965909
40 1HE 0.785185 0.955556
41 ETB 0.78125 0.9
42 COW 0.781022 0.944444
43 BYC 0.781022 0.955056
44 1GZ 0.781022 0.944444
45 FCX 0.780303 0.944444
46 CAA 0.779412 0.965909
47 4CO 0.778571 0.966292
48 0FQ 0.778571 0.977273
49 CAJ 0.777778 0.955056
50 CA6 0.776119 0.886598
51 BCA 0.775362 0.944444
52 UOQ 0.774648 0.955556
53 NHW 0.774648 0.955556
54 NHM 0.774648 0.955556
55 HAX 0.774436 0.933333
56 MC4 0.773723 0.904255
57 01A 0.77305 0.934783
58 1CZ 0.771429 0.966292
59 NMX 0.77037 0.884211
60 HXC 0.769784 0.934066
61 IRC 0.768116 0.965909
62 CS8 0.767606 0.945055
63 FAM 0.766917 0.933333
64 CA3 0.765101 0.977273
65 FAQ 0.76259 0.955056
66 NHQ 0.760274 0.988506
67 2NE 0.758865 0.934066
68 CO8 0.758865 0.934066
69 HFQ 0.756944 0.955556
70 1CV 0.755245 0.977273
71 MFK 0.753521 0.934066
72 UCC 0.753521 0.934066
73 MYA 0.753521 0.934066
74 DCC 0.753521 0.934066
75 5F9 0.753521 0.934066
76 ST9 0.753521 0.934066
77 93P 0.746753 0.988636
78 01K 0.744966 0.977273
79 MRS 0.744828 0.934066
80 MRR 0.744828 0.934066
81 WCA 0.743056 0.934066
82 CA8 0.742857 0.867347
83 YE1 0.741007 0.94382
84 DAK 0.739726 0.945055
85 HDC 0.737931 0.934066
86 4KX 0.737931 0.923913
87 8Z2 0.734694 0.923913
88 YNC 0.727891 0.944444
89 S0N 0.722222 0.955056
90 COT 0.717105 0.977273
91 1HA 0.715232 0.934066
92 F8G 0.694805 0.914894
93 93M 0.691358 0.988636
94 CA5 0.685535 0.934783
95 CCQ 0.675676 0.934783
96 7L1 0.671429 0.944444
97 CO7 0.668966 0.955056
98 UCA 0.660494 0.934066
99 COD 0.647059 0.965517
100 OXT 0.611429 0.894737
101 5TW 0.60452 0.894737
102 4BN 0.60452 0.894737
103 JBT 0.579235 0.895833
104 BSJ 0.573034 0.966667
105 PLM COA 0.572327 0.902174
106 COA PLM 0.572327 0.902174
107 HMG 0.56962 0.94382
108 ASP ASP ASP ILE CMC NH2 0.564706 0.955056
109 PAP 0.536 0.793103
110 ACE SER ASP ALY THR NH2 COA 0.518919 0.955056
111 191 0.493827 0.848485
112 PPS 0.48855 0.736842
113 A3P 0.488 0.781609
114 SFC 0.48538 0.934066
115 RFC 0.48538 0.934066
116 0WD 0.473684 0.771739
117 PTJ 0.433566 0.873563
118 3AM 0.428571 0.770115
119 WAQ 0.426573 0.862069
120 PUA 0.42236 0.802198
121 A22 0.421429 0.795455
122 PAJ 0.415493 0.885057
123 A2D 0.415385 0.784091
124 3OD 0.413793 0.827586
125 AGS 0.411765 0.788889
126 ATR 0.411765 0.781609
127 SAP 0.411765 0.788889
128 YLB 0.406452 0.909091
129 ADP 0.406015 0.804598
130 YLP 0.405229 0.88764
131 48N 0.405229 0.811111
132 A2R 0.404255 0.816092
133 F2R 0.402516 0.866667
134 NA7 0.4 0.83908
135 OAD 0.4 0.827586
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found with APoc: 183
This union binding pocket(no: 1) in the query (biounit: 1req.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 1SR9 KIV 1.72684
2 4RF7 ARG 2.04082
3 3O2K DST 2.1097
4 3B6R ADP 2.3622
5 1DJX I3P 2.40385
6 1OFZ FUL 2.5641
7 1OFZ FUC 2.5641
8 4RD0 GDP 2.6506
9 1M3U KPL 2.65152
10 4KCT PYR 2.80561
11 1U6R ADP 2.89474
12 1G51 AMP 2.93103
13 4S28 AIR 2.95139
14 4S28 SAH 2.95139
15 2JBM SRT 3.01003
16 4B0T ADP 3.24544
17 3GD9 GLC BGC BGC BGC 3.26975
18 5T9C G3P 3.35821
19 2ICK DMA 3.43348
20 3GJB AKG 3.44828
21 2VEG PMM 3.45369
22 5MRH Q9Z 3.45369
23 4FXQ G9L 3.47826
24 1O68 KIV 3.63636
25 4RW3 IPD 3.64238
26 5L2R MLA 3.64238
27 3B1Q NOS 3.68098
28 3H22 B53 3.7037
29 2CIR BG6 3.7037
30 1F9V ADP 3.7464
31 3A16 PXO 3.75335
32 5H9Y BGC BGC BGC BGC 3.82883
33 3UWV 2PG 3.83142
34 3P7N FMN 3.87597
35 1VMK GUN 3.97112
36 3U6W KIV 3.98126
37 3H55 GLA 4
38 2J5B TYE 4.02299
39 2XG5 EC5 4.04624
40 2XG5 EC2 4.04624
41 5F7J ADE 4.0625
42 4D4U FUC GAL 4.12698
43 4D4U FUC GAL NAG 4.12698
44 4D52 GXL 4.12698
45 4D52 GIV 4.12698
46 1VJ7 GPX 4.3257
47 4YJK URA 4.36508
48 5EJL C2E 4.43548
49 6CZI 38E 4.46429
50 4NZF ARB 4.46429
51 2R5V HHH 4.48179
52 2BHZ MAL 4.48505
53 6EK3 OUL 4.52489
54 1EYE PMM 4.64286
55 4HWT 1B2 4.84262
56 4V3C C 4.89691
57 5GLT BGC GAL NAG GAL 4.92958
58 4H6B 10Y 5.12821
59 4H6B 10X 5.12821
60 1H8S AIC 5.15873
61 3MI3 LYS 5.20095
62 5M77 7K2 7K3 5.26316
63 5VJE GOS 5.30726
64 5AB1 BCD TA5 HP6 MAN 5.33333
65 1GPM AMP 5.33333
66 4RT1 C2E 5.35714
67 3PGU OLA 5.38642
68 1SDW IYT 5.41401
69 2IUW AKG 5.46218
70 2IGA XXP 5.47945
71 1VRP ADP 5.51181
72 2GVJ DGB 5.70265
73 2OJW ADP 5.72917
74 2Y5S 78H 5.78231
75 4JH6 FCN 5.7971
76 2G30 ALA ALA PHE 5.81395
77 1NKI PPF 5.92593
78 4J0M BLD 5.96546
79 1OPB RET 5.97015
80 3KYF 5GP 5GP 6.06061
81 5J75 6GQ 6.06061
82 5EO8 TFU 6.10932
83 1I06 TZL 6.11111
84 4XDA RIB 6.14887
85 1MJJ HAL 6.1674
86 1F52 ADP 6.19658
87 5V3D FCN 6.2069
88 5KJW 53C 6.32318
89 5I0U DCY 6.5
90 5YSI NCA 6.57895
91 5FPE 3TR 6.71835
92 3V8S 0HD 6.82927
93 1MH5 HAL 6.84932
94 3T7V MD0 6.85714
95 4WOE ADP 6.90738
96 5N0L ILE 6.91824
97 3CBC DBS 7.07071
98 3BJE URA 7.16332
99 1Y9Q MED 7.29167
100 3UXL CFI 7.31071
101 2A5F NAD 7.42857
102 3LGS ADE 7.49064
103 3LGS SAH 7.49064
104 1EX7 5GP 7.52688
105 1GT4 UNA 7.54717
106 4BG4 ADP 7.58427
107 4LIT AKG 7.61671
108 1M5W DXP 7.81893
109 2GOO NDG 7.84314
110 5OCG 9R5 7.93651
111 5NBW 8SK 8.10811
112 4IF4 BEF 8.17308
113 5BTX CMP 8.21918
114 1DZK PRZ 8.28025
115 4RYV ZEA 8.3871
116 5DYO FLU 8.49057
117 3H0L ADP 8.51064
118 3THR C2F 8.53242
119 1X9I G6Q 8.60927
120 5YRV 5AD 8.66426
121 6FA4 D1W 8.67052
122 2Z3U CRR 8.70588
123 2Y7P SAL 8.7156
124 5GP0 GPP 8.72483
125 5LUN OGA 8.80682
126 4JN6 OXL 8.82353
127 4P7U 1PS 8.92857
128 2C49 ADN 8.9404
129 2P7Q GG6 9.02256
130 1KTC NGA 9.1358
131 2ZSC BTN 9.21986
132 1J3R 6PG 9.47368
133 5YJS SAL 9.48718
134 2ZMF CMP 9.52381
135 5F6U 5VK 9.55414
136 4Y24 TD2 9.74026
137 2C3W GLC GLC GLC GLC 9.80392
138 2E27 AB0 10.084
139 1ZOT EMA 10.1449
140 3ZGJ RMN 10.2426
141 6GNO XDI 10.3704
142 4B5W PYR 10.5469
143 3SAO DBH 10.625
144 3SAO NKN 10.625
145 2VDF OCT 10.6719
146 5H9P TD2 10.7595
147 4FK7 P34 10.917
148 5Y4R C2E 11.0345
149 5W75 SUC 11.2245
150 5XEG AKG 11.2554
151 4OCT AKG 11.2613
152 6BU0 IHP 11.4504
153 3ZW0 FUC 11.4943
154 3ZW2 GAL FUC 11.4943
155 3ZW2 NAG GAL FUC 11.4943
156 1ZNY GDP 11.5942
157 3WG3 A2G GAL NAG FUC 11.7978
158 1Y7P RIP 12.5561
159 3JQ3 ADP 12.8415
160 1WW5 SGA BGC 13.125
161 6F7X MFU 13.3333
162 2BS5 BGC GAL FUC 13.3333
163 6CLV 6MB 13.4021
164 3ESS 18N 13.4783
165 1P0Z FLC 13.7405
166 3ZO7 K6H 13.8298
167 3NZ1 3NY 14.1762
168 2YKL NLD 14.3519
169 4B1M FRU FRU 15.1351
170 5XQW 8EU 15.2074
171 2YIP YIO 15.942
172 1IIU RTL 16.092
173 4COQ SAN 16.1943
174 4B1L FRU 16.9697
175 4CSD MFU 17.2794
176 2RDE C2E 17.9283
177 3M3E GAL A2G NPO 18.0124
178 2FKA BEF 18.6047
179 2TPI ILE VAL 18.7773
180 1UGY GLA BGC 20
181 4BJ8 BTN 20.6349
182 2BOS GLA GAL 29.4118
183 4M1U A2G MBG 30
Pocket No.: 2; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found with APoc: 30
This union binding pocket(no: 2) in the query (biounit: 1req.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 1OFL NGK GCD 1.8711
3 2VQ5 HBA 2.98507
4 4IP7 FLC 3.13075
5 3JU6 ANP 3.24324
6 1S5O 152 3.57143
7 1ELI PYC 3.59897
8 5INJ 6C7 4.19753
9 5VZ0 ADP 4.23862
10 2BMB PMM 4.40367
11 6BYM HC3 4.4335
12 3GM5 CIT 5.03145
13 1GPM CIT 5.33333
14 2CI5 HCS 5.6338
15 1NVM OXL 6.08974
16 6G9I CXX 6.66667
17 1VKF CIT 6.91489
18 5N0F 7K2 7.45856
19 1USF NAP 7.86517
20 1F5F DHT 9.26829
21 4EE7 PIS 9.53947
22 3HP8 SUC 10
23 5KY9 GDP 11.5493
24 1QD1 FON 12
25 2VFT SOR 12.0853
26 1L5Y BEF 13.5484
27 2OMN IPH 14.7465
28 5KEW 6SB 15.9574
29 6BR7 BEF 20.3008
30 1RZX ACE VAL LYS GLU SER LEU VAL 20.4082
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