FAIRMol

Z56071437

Pose ID 8035 Compound 311 Pose 583

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 Z56071437
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
27.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.88, Jaccard 0.78, H-bond role recall 0.50
Burial
68%
Hydrophobic fit
70%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.859 kcal/mol/HA) ✓ Good fit quality (FQ -8.37) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (27.1 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (12) ✗ Many internal clashes (14)
Score
-26.640
kcal/mol
LE
-0.859
kcal/mol/HA
Fit Quality
-8.37
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
5.50
cLogP
Strain ΔE
27.1 kcal/mol
SASA buried
68%
Lipo contact
70% BSA apolar/total
SASA unbound
743 Ų
Apolar buried
355 Ų

Interaction summary

HB 9 HY 7 PI 4 CLASH 6 ⚠ Exposure 38%
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21 Buried (contacted) 13 Exposed 8 LogP 5.5 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank2.606Score-26.640
Inter norm-0.895Intra norm0.035
Top1000noExcludedno
Contacts16H-bonds9
Artifact reasongeometry warning; 14 clashes; 12 protein contact clashes; moderate strain Δ 27.1
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG46 ASP13 CYS72 GLY73 HIS14 ILE15 ILE76 SER74 TYR49

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
Jaccard0.78RMSD-
HB strict7Strict recall0.58
HB same residue+role5HB role recall0.50
HB same residue5HB residue recall0.50

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
572 0.5870117947832066 -1.10765 -37.5989 7 16 0 0.00 0.00 - no Open
583 0.8823549273857154 -0.910836 -30.2227 2 20 0 0.00 0.00 - no Open
592 1.310495564240597 -0.754262 -27.3292 4 16 0 0.00 0.00 - no Open
611 1.7798849023795245 -0.802683 -26.2147 4 16 0 0.00 0.00 - no Open
594 1.9412230667148331 -0.877204 -32.0703 1 19 0 0.00 0.00 - no Open
584 2.0822003114507757 -0.856641 -25.7246 2 18 0 0.00 0.00 - no Open
583 2.606119674997513 -0.894636 -26.6402 9 16 14 0.88 0.50 - no Current
600 2.62217074979796 -0.689693 -24.6956 3 8 0 0.00 0.00 - no Open
575 3.3580502961066707 -0.8137 -25.6478 3 15 0 0.00 0.00 - no Open
595 3.5009994029016003 -0.774293 -24.4273 4 21 0 0.00 0.00 - no Open
587 3.744243536944524 -0.642671 -23.6962 5 10 0 0.00 0.00 - no Open
600 3.987159201366124 -1.08362 -33.2245 13 19 0 0.00 0.00 - no Open
591 6.027892840267617 -0.912188 -27.1412 8 19 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 -26.640kcal/mol
Ligand efficiency (LE) -0.8594kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.372
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 500.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.50
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -30.10kcal/mol
Minimised FF energy -57.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 743.0Ų
Total solvent-accessible surface area of free ligand
BSA total 506.4Ų
Buried surface area upon binding
BSA apolar 355.1Ų
Hydrophobic contacts buried
BSA polar 151.3Ų
Polar contacts buried
Fraction buried 68.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2240.0Ų
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 803.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)