FAIRMol

Z653345210

Pose ID 7861 Compound 2087 Pose 409

DB fairmolDocking 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 Z653345210
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
4.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.69, Jaccard 0.58, H-bond role recall 0.40
Burial
76%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (4.8 kcal/mol) ✓ Excellent LE (-1.059 kcal/mol/HA) ✓ Good fit quality (FQ -9.49) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-25.426
kcal/mol
LE
-1.059
kcal/mol/HA
Fit Quality
-9.49
FQ (Leeson)
HAC
24
heavy atoms
MW
337
Da
LogP
2.83
cLogP
Final rank
3.8793
rank score
Inter norm
-1.176
normalised
Contacts
14
H-bonds 13
Strain ΔE
4.8 kcal/mol
SASA buried
76%
Lipo contact
72% BSA apolar/total
SASA unbound
591 Ų
Apolar buried
324 Ų

Interaction summary

HBA 6 HY 4 PI 3 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap11Native recall0.69
Jaccard0.58RMSD-
HB strict6Strict recall0.50
HB same residue+role4HB role recall0.40
HB same residue4HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
102 1.7316048619282671 -1.26112 -28.1611 6 13 0 0.00 0.00 - no Open
409 3.8792717208930334 -1.17631 -25.4259 13 14 11 0.69 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 -25.426kcal/mol
Ligand efficiency (LE) -1.0594kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.494
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.83
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 4.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 36.82kcal/mol
Minimised FF energy 31.99kcal/mol

SASA & burial

✓ computed
SASA (unbound) 591.2Ų
Total solvent-accessible surface area of free ligand
BSA total 452.4Ų
Buried surface area upon binding
BSA apolar 324.1Ų
Hydrophobic contacts buried
BSA polar 128.2Ų
Polar contacts buried
Fraction buried 76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2134.5Ų
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 774.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)