FAIRMol

Z56815073

Pose ID 4725 Compound 318 Pose 662

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T07
T. brucei PTR1 T. brucei
Ligand Z56815073
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.3 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.73, H-bond role recall 0.00
Burial
84%
Hydrophobic fit
78%
Reason: strain 43.3 kcal/mol
strain ΔE 43.3 kcal/mol 2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.895 kcal/mol/HA) ✓ Good fit quality (FQ -8.80) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (43.3 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (11)
Score
-28.652
kcal/mol
LE
-0.895
kcal/mol/HA
Fit Quality
-8.80
FQ (Leeson)
HAC
32
heavy atoms
MW
569
Da
LogP
5.67
cLogP
Final rank
0.6662
rank score
Inter norm
-1.040
normalised
Contacts
19
H-bonds 3
Strain ΔE
43.3 kcal/mol
SASA buried
84%
Lipo contact
78% BSA apolar/total
SASA unbound
744 Ų
Apolar buried
486 Ų

Interaction summary

HB 0 HY 10 PI 6 CLASH 3

HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) detected for this pose.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap16Native recall0.84
Jaccard0.73RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU: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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
662 0.6661725537921506 -1.04002 -28.6522 3 19 16 0.84 0.00 - no Current
659 0.7707737947628458 -0.753505 -21.1708 0 16 0 0.00 0.00 - no Open
652 0.8225922751736459 -1.01993 -29.9798 1 17 15 0.79 0.00 - no Open
642 1.139808952940768 -0.847734 -26.7285 5 14 0 0.00 0.00 - no Open
656 1.7653889637304623 -0.867492 -24.6089 3 18 0 0.00 0.00 - no Open
655 1.8473635475241321 -1.0072 -32.0974 3 18 0 0.00 0.00 - no Open
638 1.9648568381193203 -0.927569 -29.9449 4 16 0 0.00 0.00 - no Open
645 2.1923496622071084 -0.758001 -17.56 2 18 0 0.00 0.00 - no Open
661 2.2567473265764555 -0.765666 -25.1725 7 20 0 0.00 0.00 - no Open
641 2.292373942513122 -0.725642 -22.2969 4 13 0 0.00 0.00 - no Open
641 2.2974884616866427 -0.933418 -28.8424 4 19 0 0.00 0.00 - no Open
654 3.071439811116401 -0.870778 -29.2301 13 16 0 0.00 0.00 - no Open
659 3.8692944863611776 -0.656079 -21.7278 6 10 0 0.00 0.00 - no Open
660 3.931763085408765 -0.81696 -27.3427 3 19 0 0.00 0.00 - no Open
666 5.297500006745246 -0.919049 -23.1364 13 21 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -28.652kcal/mol
Ligand efficiency (LE) -0.8954kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.805
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 568.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.67
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 42.84kcal/mol
Minimised FF energy -0.42kcal/mol

SASA & burial

✓ computed
SASA (unbound) 743.5Ų
Total solvent-accessible surface area of free ligand
BSA total 620.6Ų
Buried surface area upon binding
BSA apolar 486.1Ų
Hydrophobic contacts buried
BSA polar 134.5Ų
Polar contacts buried
Fraction buried 83.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1681.6Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 936.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)