FAIRMol

Z20248532

Pose ID 5981 Compound 1279 Pose 563

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
T09
L. major DHFR-TS L. major
Ligand Z20248532

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
19.2 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.67, Jaccard 0.67, H-bond role recall 0.33
Burial
75%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes 36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.748 kcal/mol/HA) ✓ Good fit quality (FQ -7.36) ✓ Good H-bonds (4 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (19.2 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (5)
Score
-23.942
kcal/mol
LE
-0.748
kcal/mol/HA
Fit Quality
-7.36
FQ (Leeson)
HAC
32
heavy atoms
MW
466
Da
LogP
3.91
cLogP
Final rank
0.5944
rank score
Inter norm
-0.787
normalised
Contacts
14
H-bonds 4
Strain ΔE
19.2 kcal/mol
SASA buried
75%
Lipo contact
68% BSA apolar/total
SASA unbound
710 Ų
Apolar buried
360 Ų

Interaction summary

HBD 1 HBA 3 HY 5 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap14Native recall0.67
Jaccard0.67RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.33

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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
563 0.5944353098358637 -0.787419 -23.9417 4 14 14 0.67 0.33 - no Current
574 2.3067505993748267 -0.834626 -24.8595 7 13 0 0.00 0.00 - no Open
585 2.5151408113601668 -0.724038 -21.2913 6 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 -23.942kcal/mol
Ligand efficiency (LE) -0.7482kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.358
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 465.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.91
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 55.60kcal/mol
Minimised FF energy 36.39kcal/mol

SASA & burial

✓ computed
SASA (unbound) 710.3Ų
Total solvent-accessible surface area of free ligand
BSA total 531.2Ų
Buried surface area upon binding
BSA apolar 359.9Ų
Hydrophobic contacts buried
BSA polar 171.3Ų
Polar contacts buried
Fraction buried 74.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3280.4Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1674.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)