FAIRMol

Z56815073

Pose ID 8106 Compound 318 Pose 654

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 Z56815073
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
36.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.30
Burial
73%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.913 kcal/mol/HA) ✓ Good fit quality (FQ -8.98) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (36.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-29.230
kcal/mol
LE
-0.913
kcal/mol/HA
Fit Quality
-8.98
FQ (Leeson)
HAC
32
heavy atoms
MW
569
Da
LogP
6.24
cLogP
Strain ΔE
36.8 kcal/mol
SASA buried
73%
Lipo contact
76% BSA apolar/total
SASA unbound
707 Ų
Apolar buried
395 Ų

Interaction summary

HB 13 HY 6 PI 1 CLASH 3 ⚠ Exposure 47%

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
⚠️Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21 Buried (contacted) 11 Exposed 10 LogP 6.24 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.071Score-29.230
Inter norm-0.871Intra norm-0.043
Top1000noExcludedno
Contacts16H-bonds13
Artifact reasongeometry warning; 13 clashes; 1 protein clash; high strain Δ 36.8
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 ASP13 GLY73 GLY77 HIS14 ILE15 SER74 TYR49

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 overlap13Native recall0.81
Jaccard0.68RMSD-
HB strict4Strict recall0.33
HB same residue+role3HB role recall0.30
HB same residue3HB residue recall0.30

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
662 0.6661725537921506 -1.04002 -28.6522 3 19 0 0.00 0.00 - no Open
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 0 0.00 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 13 0.81 0.30 - no Current
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 -29.230kcal/mol
Ligand efficiency (LE) -0.9134kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.983
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 568.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.24
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.46kcal/mol
Minimised FF energy 22.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 706.7Ų
Total solvent-accessible surface area of free ligand
BSA total 518.3Ų
Buried surface area upon binding
BSA apolar 394.9Ų
Hydrophobic contacts buried
BSA polar 123.4Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2198.7Ų
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 784.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)