FAIRMol

Z24585638

Pose ID 2020 Compound 1204 Pose 665

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
T03
L. major DHFR L. major
Ligand Z24585638

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
15.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.71, H-bond role recall 0.20
Burial
87%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.943 kcal/mol/HA) ✓ Good fit quality (FQ -9.00) ✓ Good H-bonds (3 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (15.7 kcal/mol) ✗ Geometry warnings
Score
-27.353
kcal/mol
LE
-0.943
kcal/mol/HA
Fit Quality
-9.00
FQ (Leeson)
HAC
29
heavy atoms
MW
428
Da
LogP
5.38
cLogP
Strain ΔE
15.7 kcal/mol
SASA buried
87%
Lipo contact
77% BSA apolar/total
SASA unbound
693 Ų
Apolar buried
464 Ų

Interaction summary

HB 3 HY 24 PI 3 CLASH 3

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 rank1.875Score-27.353
Inter norm-1.054Intra norm0.110
Top1000noExcludedno
Contacts16H-bonds3
Artifact reasongeometry warning; 4 clashes; 1 protein clash
Residues
ALA32 ARG97 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 THR83 TYR162 VAL156 VAL30 VAL31 VAL87

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap15Native recall0.75
Jaccard0.71RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; 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
653 1.3461306924792613 -0.897843 -18.079 4 17 1 0.05 0.00 - no Open
665 1.8748858058976448 -1.05367 -27.3534 3 16 15 0.75 0.20 - no Current
669 2.284235244877461 -0.973642 -26.787 3 13 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 -27.353kcal/mol
Ligand efficiency (LE) -0.9432kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.004
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.38
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.85kcal/mol
Minimised FF energy 42.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.4Ų
Total solvent-accessible surface area of free ligand
BSA total 606.1Ų
Buried surface area upon binding
BSA apolar 464.1Ų
Hydrophobic contacts buried
BSA polar 142.1Ų
Polar contacts buried
Fraction buried 87.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1542.7Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 821.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)