FAIRMol

Z56768366

Pose ID 5252 Compound 194 Pose 511

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
T08
T. brucei PTR1 T. brucei
Ligand Z56768366
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
34.8 kcal/mol
Protein clashes
5
Internal clashes
7
Native overlap
contact recall 0.74, Jaccard 0.61, H-bond role recall 0.20
Burial
98%
Hydrophobic fit
86%
Reason: 7 internal clashes
5 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.914 kcal/mol/HA) ✓ Good fit quality (FQ -8.72) ✓ Good H-bonds (4 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Very high strain energy (34.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (15)
Score
-26.494
kcal/mol
LE
-0.914
kcal/mol/HA
Fit Quality
-8.72
FQ (Leeson)
HAC
29
heavy atoms
MW
426
Da
LogP
5.37
cLogP
Strain ΔE
34.8 kcal/mol
SASA buried
98%
Lipo contact
86% BSA apolar/total
SASA unbound
643 Ų
Apolar buried
544 Ų

Interaction summary

HB 4 HY 24 PI 3 CLASH 7
Final rank1.237Score-26.494
Inter norm-1.203Intra norm0.290
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 15 clashes; 5 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 34.8
Residues
ARG14 ASN175 ASP161 CYS168 GLY205 LEU208 LEU209 MET163 NAP301 PHE171 PHE97 PRO167 PRO210 SER207 TRP221 TYR174 VAL164 VAL206

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
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

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 overlap14Native recall0.74
Jaccard0.61RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
487 1.088329866091016 -1.17165 -32.6657 5 19 17 0.89 0.40 - no Open
511 1.2374971441566485 -1.20348 -26.4937 4 18 14 0.74 0.20 - no Current
548 1.4904529892984921 -0.920653 -22.5653 9 17 0 0.00 0.00 - no Open
521 1.81825799653337 -0.897538 -26.5745 4 17 0 0.00 0.00 - no Open
565 2.2544588790717133 -0.826268 -25.3055 8 11 0 0.00 0.00 - no Open
530 2.3192700841994296 -0.96341 -25.2468 1 20 0 0.00 0.00 - no Open
512 2.4932728018700403 -1.10026 -30.6157 5 16 0 0.00 0.00 - no Open
541 2.508845732894417 -0.876449 -24.5843 1 18 0 0.00 0.00 - no Open
522 2.531497306555514 -0.838818 -22.236 1 15 0 0.00 0.00 - no Open
543 2.556193085876479 -0.766219 -16.5141 5 18 0 0.00 0.00 - no Open
503 2.6989153506438197 -0.909917 -24.0506 6 16 0 0.00 0.00 - no Open
508 3.0900948345735757 -0.897584 -21.3907 7 15 0 0.00 0.00 - no Open
516 3.307089045836197 -0.707354 -18.8371 3 12 0 0.00 0.00 - no Open
499 3.642356120158013 -1.12423 -30.5543 8 18 0 0.00 0.00 - no Open
511 3.6596004503079134 -0.851044 -25.8511 6 13 0 0.00 0.00 - no Open
504 4.110164392350293 -1.09071 -27.3774 9 16 0 0.00 0.00 - no Open
550 4.159361593789174 -0.833109 -22.8091 6 11 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 -26.494kcal/mol
Ligand efficiency (LE) -0.9136kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.721
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 425.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.37
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 42.87kcal/mol
Minimised FF energy 8.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.8Ų
Total solvent-accessible surface area of free ligand
BSA total 632.4Ų
Buried surface area upon binding
BSA apolar 544.2Ų
Hydrophobic contacts buried
BSA polar 88.2Ų
Polar contacts buried
Fraction buried 98.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1682.9Ų
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 923.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)