FAIRMol

Z19455379

Pose ID 3772 Compound 2584 Pose 386

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
T06
T. brucei DHFR T. brucei
Ligand Z19455379
PDB8RHT↗

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 high Native strong SASA done
Strain ΔE
16.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.25
Burial
96%
Hydrophobic fit
56%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.843 kcal/mol/HA) ✓ Good fit quality (FQ -7.55) ✓ Good H-bonds (5 bonds) ✓ Deep burial (96% SASA buried) ✗ Moderate strain (16.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-20.221
kcal/mol
LE
-0.843
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
24
heavy atoms
MW
344
Da
LogP
1.88
cLogP
Strain ΔE
16.0 kcal/mol
SASA buried
96%
Lipo contact
56% BSA apolar/total
SASA unbound
583 Ų
Apolar buried
317 Ų

Interaction summary

HB 5 HY 24 PI 1 CLASH 2

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
Final rank1.839Score-20.221
Inter norm-1.012Intra norm0.170
Top1000noExcludedno
Contacts18H-bonds5
Artifact reasongeometry warning; 5 clashes; 1 protein clash
Residues
ALA34 ARG100 ARG59 ASP54 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 THR184 TYR166 TYR57 VAL32 VAL33

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap16Native recall0.76
Jaccard0.70RMSD-
HB strict1Strict recall0.20
HB same residue+role1HB role recall0.25
HB same residue2HB residue recall0.50

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
386 1.839433879338239 -1.01234 -20.2213 5 18 16 0.76 0.25 - no Current
378 2.854415706722772 -1.19654 -26.2923 15 14 0 0.00 0.00 - no Open
400 3.2741913472875535 -1.30243 -26.8389 11 18 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 -20.221kcal/mol
Ligand efficiency (LE) -0.8426kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.551
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.88
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 64.32kcal/mol
Minimised FF energy 48.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 583.1Ų
Total solvent-accessible surface area of free ligand
BSA total 561.4Ų
Buried surface area upon binding
BSA apolar 316.8Ų
Hydrophobic contacts buried
BSA polar 244.6Ų
Polar contacts buried
Fraction buried 96.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 56.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1568.3Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 578.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)