Docking pose detail

Molecular metrics status: missing

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T08

T. brucei PTR1 T. brucei

Ligand Z49630783

PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak Metrics pending

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA pending

Strain ΔE

61.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.63, Jaccard 0.55, H-bond role recall 0.40

Burial

95%

Reason: strain 61.9 kcal/mol

strain ΔE 61.9 kcal/mol 3 protein-contact clashes 4 intramolecular clashes

Interaction summary

HB 8 HY 24 PI 2 CLASH 4

HB · H-bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Final rank	2.125	Score	-27.016
Inter norm	-1.140	Intra norm	0.264
Top1000	no	Excluded	yes
Contacts	15	H-bonds	8
Artifact reason	excluded; hard geometry fail; 1 severe clash; 5 protein contact clashes; 3 cofactor-context clashes; high strain Δ 61.9
Residues	ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS13 MET163 NAP301 PHE97 PRO210 TRP221 TYR174 VAL206 VAL211

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	TbPTR1_cW_6RX6_Ready	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap	12	Native recall	0.63
Jaccard	0.55	RMSD	-
HB strict	2	Strict recall	0.33
HB same residue+role	2	HB role recall	0.40
HB same residue	3	HB residue recall	0.60

Protein summary

258 residues

Protein target	T08	Atoms	3881
Residues	258	Chains	2
Residue summary	LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:NAP301

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
487	2.125329754062828	-1.13995	-27.0157	8	15	12	0.63	0.40	-	yes	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

⚠ Not yet computed

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