FAIRMol

Z46089428

Pose ID 7942 Compound 1100 Pose 490

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
T12
T. brucei R5P T. brucei
Ligand Z46089428
PDB6FXS↗

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
33.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.40
Burial
68%
Hydrophobic fit
72%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 40% of hydrophobic surface appears solvent-exposed (12/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.703 kcal/mol/HA) ✓ Good fit quality (FQ -7.14) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (33.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (11) ✗ Many internal clashes (16)
Score
-25.296
kcal/mol
LE
-0.703
kcal/mol/HA
Fit Quality
-7.14
FQ (Leeson)
HAC
36
heavy atoms
MW
475
Da
LogP
5.26
cLogP
Strain ΔE
33.0 kcal/mol
SASA buried
68%
Lipo contact
72% BSA apolar/total
SASA unbound
792 Ų
Apolar buried
393 Ų

Interaction summary

HB 8 HY 14 PI 2 CLASH 6 ⚠ Exposure 40%
⚠️Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (12/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30 Buried (contacted) 18 Exposed 12 LogP 5.26 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank2.649Score-25.296
Inter norm-0.897Intra norm0.193
Top1000noExcludedno
Contacts20H-bonds8
Artifact reasongeometry warning; 16 clashes; 11 protein contact clashes; moderate strain Δ 29.8
Residues
ARG140 ARG144 ASN106 GLU138 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 ASP13 ASP48 CYS72 GLY73 GLY77 HIS14 ILE15 SER74 TYR49 VAL47

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap14Native recall0.88
Jaccard0.64RMSD-
HB strict5Strict recall0.42
HB same residue+role4HB role recall0.40
HB same residue4HB residue recall0.40

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
519 1.177333702061779 -0.758263 -22.7147 3 18 0 0.00 0.00 - no Open
557 1.609109162871771 -0.685578 -24.5307 4 17 0 0.00 0.00 - no Open
490 2.649443862709782 -0.896526 -25.2964 8 20 14 0.88 0.40 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -25.296kcal/mol
Ligand efficiency (LE) -0.7027kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.142
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.26
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 8.75kcal/mol
Minimised FF energy -24.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 791.6Ų
Total solvent-accessible surface area of free ligand
BSA total 542.3Ų
Buried surface area upon binding
BSA apolar 393.2Ų
Hydrophobic contacts buried
BSA polar 149.2Ų
Polar contacts buried
Fraction buried 68.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2285.7Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 798.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)