Receptor
PDB id Resolution Class Description Source Keywords
4MUQ 1.36 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE V COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG ENTEROCOCCUS FAECALIS CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES CSGIDNATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES NIAIALPHA+BETA PROTEIN METALLOPEPTIDASE HEDGEHOG/DD-PEPTIDASEMEROPS M15B SUBFAMILY ZN2+-DEPENDENT DD-DIPEPTIDASE VANCRESISTANCE ANTIBIOTIC RESISTANCE HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE EVOLUTION OF VANCOMYCIN RE D,D-PEPTIDASES. PROC.NATL.ACAD.SCI.USA V. 111 5872 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:305;
A:306;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PE3 A:307;
A:309;
A:308;
A:310;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
634.751 C28 H58 O15 C(COC...
EDO A:304;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
LY0 A:302;
Valid;
none;
submit data
195.153 C6 H14 N O4 P C[C@@...
ZN A:301;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
2D8 A:303;
Valid;
none;
submit data
195.153 C6 H14 N O4 P C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MUQ 1.36 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE V COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG ENTEROCOCCUS FAECALIS CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES CSGIDNATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES NIAIALPHA+BETA PROTEIN METALLOPEPTIDASE HEDGEHOG/DD-PEPTIDASEMEROPS M15B SUBFAMILY ZN2+-DEPENDENT DD-DIPEPTIDASE VANCRESISTANCE ANTIBIOTIC RESISTANCE HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE EVOLUTION OF VANCOMYCIN RE D,D-PEPTIDASES. PROC.NATL.ACAD.SCI.USA V. 111 5872 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 4MUQ - LY0 C6 H14 N O4 P C[C@@H](C[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 4MUQ - LY0 C6 H14 N O4 P C[C@@H](C[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 4MUQ - LY0 C6 H14 N O4 P C[C@@H](C[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LY0; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 LY0 1 1
2 2D8 1 1
3 AEP 0.594595 0.842105
4 P8D 0.552632 0.914286
5 PHY 0.5 0.8
Ligand no: 2; Ligand: 2D8; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 LY0 1 1
2 2D8 1 1
3 AEP 0.594595 0.842105
4 P8D 0.552632 0.914286
5 PHY 0.5 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: LY0; Similar ligands found: 141
No: Ligand Similarity coefficient
1 DAL DAL 0.9378
2 SYM 0.9319
3 8GL 0.9283
4 UN1 0.9238
5 HFA 0.9197
6 RAT 0.9190
7 PHE 0.9189
8 2FT 0.9153
9 3LR 0.9142
10 GLU 0.9118
11 LFC 0.9107
12 PEP 0.9098
13 GRO 0.9091
14 APG 0.9081
15 AKG 0.9075
16 0OC 0.9074
17 R2P 0.9064
18 GCO 0.9058
19 SPV 0.9050
20 LYS 0.9047
21 DLY 0.9047
22 PPR 0.9044
23 REL 0.9039
24 4WK 0.9025
25 HL5 0.9020
26 DXG 0.9017
27 AL0 0.9015
28 FK8 0.8991
29 KDG 0.8990
30 SOR 0.8983
31 SEP 0.8980
32 GLN 0.8972
33 X1R 0.8964
34 2PG 0.8958
35 2HG 0.8953
36 I38 0.8953
37 S2G 0.8940
38 TIH 0.8929
39 DHI 0.8928
40 ICT 0.8926
41 3SL 0.8923
42 DGL 0.8922
43 2IT 0.8922
44 CXP 0.8916
45 B3U 0.8914
46 HDL 0.8909
47 CS2 0.8903
48 MTL 0.8898
49 P58 0.8897
50 GAE 0.8894
51 3PG 0.8892
52 SMN 0.8891
53 DPN 0.8885
54 0V5 0.8884
55 EDR 0.8881
56 SAF 0.8881
57 ALA ALA 0.8876
58 C5A 0.8871
59 7OD 0.8868
60 DGN 0.8862
61 XSP 0.8862
62 XYH 0.8857
63 5ZZ 0.8856
64 GGB 0.8848
65 RMN 0.8847
66 MHO 0.8846
67 HGA 0.8846
68 OOG 0.8839
69 SOL 0.8836
70 GZ3 0.8835
71 AFS 0.8833
72 LGT 0.8826
73 3HP 0.8823
74 SHI 0.8823
75 Q03 0.8823
76 S2P 0.8822
77 HF2 0.8821
78 9ON 0.8818
79 9RW 0.8816
80 K6H 0.8812
81 AHN 0.8807
82 6FZ 0.8805
83 OSE 0.8799
84 PEQ 0.8793
85 ONL 0.8786
86 9YT 0.8779
87 XIZ 0.8779
88 0L1 0.8775
89 NFA 0.8770
90 LYN 0.8764
91 GLO 0.8759
92 API 0.8757
93 3BU 0.8747
94 9RH 0.8743
95 SER THR 0.8740
96 HPV 0.8740
97 HA5 0.8738
98 P22 0.8734
99 HL4 0.8731
100 7A3 0.8729
101 CUW 0.8725
102 R67 0.8720
103 3MV 0.8716
104 LUQ 0.8710
105 QMP 0.8707
106 XLS 0.8705
107 FIX 0.8702
108 LEU 0.8699
109 XYL 0.8698
110 RB5 0.8698
111 SME 0.8697
112 LLH 0.8695
113 8SZ 0.8690
114 ORN 0.8690
115 PSJ 0.8690
116 RUJ 0.8686
117 8OZ 0.8680
118 HG3 0.8678
119 E4P 0.8677
120 DIR 0.8659
121 DZA 0.8659
122 G3H 0.8650
123 7BC 0.8646
124 1GP 0.8634
125 NLQ 0.8614
126 G2H 0.8612
127 G3P 0.8612
128 ACH 0.8607
129 9J3 0.8606
130 OAF 0.8605
131 2JJ 0.8589
132 RNT 0.8588
133 GLR 0.8583
134 NLE 0.8573
135 RNS 0.8563
136 SDD 0.8556
137 5FX 0.8554
138 SHV 0.8523
139 CHH 0.8521
140 TPO 0.8514
141 NNH 0.8512
Ligand no: 2; Ligand: 2D8; Similar ligands found: 195
No: Ligand Similarity coefficient
1 SYM 0.9369
2 DAL DAL 0.9296
3 X1R 0.9239
4 HFA 0.9236
5 8GL 0.9203
6 HHH 0.9190
7 173 0.9166
8 PHE 0.9163
9 OGA 0.9149
10 GLU 0.9133
11 HIS 0.9121
12 UN1 0.9108
13 FA1 0.9098
14 PEP 0.9094
15 RAT 0.9092
16 R2P 0.9083
17 KDG 0.9081
18 GRO 0.9080
19 2FT 0.9075
20 DGL 0.9074
21 AKG 0.9067
22 GCO 0.9065
23 PPY 0.9063
24 3MV 0.9061
25 3LR 0.9059
26 I38 0.9057
27 NCT 0.9052
28 PPR 0.9049
29 SPV 0.9046
30 SMN 0.9044
31 OOG 0.9034
32 HL5 0.9028
33 AL0 0.9027
34 9YT 0.9018
35 P22 0.9017
36 3PG 0.9012
37 61M 0.9008
38 S2G 0.9007
39 APG 0.9005
40 LYS 0.8994
41 DLY 0.8994
42 SAF 0.8991
43 B09 0.8988
44 DXG 0.8988
45 9ON 0.8987
46 ALA ALA 0.8979
47 2PG 0.8978
48 REL 0.8977
49 4WK 0.8974
50 A09 0.8973
51 CS2 0.8970
52 K6H 0.8969
53 SOR 0.8966
54 GGL 0.8966
55 A29 0.8958
56 2HG 0.8949
57 DGN 0.8944
58 FEH 0.8944
59 MTL 0.8941
60 7OD 0.8939
61 FK8 0.8920
62 R67 0.8920
63 SME 0.8919
64 DHI 0.8914
65 GLN 0.8914
66 CXP 0.8905
67 HGA 0.8904
68 OSE 0.8903
69 0L1 0.8902
70 EDR 0.8900
71 DPN 0.8898
72 HG3 0.8898
73 TIH 0.8892
74 2IT 0.8888
75 HF2 0.8885
76 SHI 0.8881
77 GAE 0.8880
78 ISZ 0.8870
79 LFC 0.8867
80 0V5 0.8865
81 XSP 0.8864
82 13P 0.8863
83 FUD 0.8859
84 QUS 0.8858
85 E4P 0.8853
86 HDH 0.8848
87 HPV 0.8846
88 5ZZ 0.8846
89 C5A 0.8839
90 9RW 0.8836
91 A3M 0.8835
92 SEP 0.8832
93 9RH 0.8828
94 3YP 0.8823
95 LNR 0.8818
96 BHU 0.8817
97 ONL 0.8814
98 S2P 0.8813
99 HL4 0.8812
100 DZA 0.8808
101 HA5 0.8806
102 LYN 0.8804
103 KTA 0.8803
104 MHO 0.8801
105 API 0.8800
106 NFA 0.8800
107 BHO 0.8798
108 HDL 0.8795
109 Q03 0.8794
110 SER THR 0.8786
111 8OZ 0.8786
112 LUQ 0.8786
113 I1E 0.8784
114 GZ3 0.8780
115 NLE 0.8776
116 GLR 0.8775
117 LX1 0.8772
118 3CR 0.8769
119 RMN 0.8769
120 8SZ 0.8769
121 RUJ 0.8768
122 KMH 0.8766
123 MSE 0.8764
124 MZT 0.8764
125 XYH 0.8757
126 AMQ 0.8755
127 2JJ 0.8754
128 DIR 0.8753
129 XYL 0.8750
130 RB5 0.8750
131 9J3 0.8750
132 GLO 0.8748
133 6FZ 0.8747
134 MET 0.8746
135 NIZ 0.8745
136 AFS 0.8744
137 J9T 0.8740
138 B3U 0.8738
139 TLA 0.8733
140 PEQ 0.8732
141 F9P 0.8725
142 LGT 0.8720
143 TPO 0.8714
144 LEU 0.8709
145 B40 0.8707
146 23J 0.8703
147 XLS 0.8697
148 QMP 0.8693
149 PO6 0.8689
150 TZL 0.8686
151 ORN 0.8682
152 CFI 0.8678
153 AVI 0.8676
154 F98 0.8676
155 SOL 0.8674
156 7UC 0.8673
157 MCO 0.8667
158 TAG 0.8666
159 791 0.8658
160 MES 0.8656
161 Q9Z 0.8656
162 BRH 0.8651
163 1GP 0.8651
164 CCE 0.8647
165 G3P 0.8644
166 PC 0.8643
167 7BC 0.8642
168 PSJ 0.8641
169 Q04 0.8640
170 LLH 0.8638
171 3BU 0.8638
172 069 0.8632
173 LPK 0.8627
174 ACH 0.8626
175 XUL 0.8624
176 DER 0.8620
177 92K 0.8617
178 0A9 0.8610
179 152 0.8609
180 7C3 0.8607
181 DYT 0.8606
182 ACA 0.8605
183 P7Y 0.8594
184 LMR 0.8588
185 RNS 0.8587
186 KPA 0.8587
187 G3H 0.8583
188 HNK 0.8578
189 JF6 0.8573
190 GP9 0.8564
191 DII 0.8562
192 SRT 0.8558
193 IP8 0.8549
194 ILO 0.8543
195 PGH 0.8541
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MUQ; Ligand: 2D8; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4muq.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZHW DAL DAL 41.6667
2 6A6A DAL 42.2222
Pocket No.: 2; Query (leader) PDB : 4MUQ; Ligand: LY0; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 4muq.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZHW DAL DAL 41.6667
2 6A6A DAL 42.2222
3 6A6A DAL 42.2222
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