FAIRMol

CKP-41

Pose ID 5670 Compound 121 Pose 252

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
T09
L. major DHFR-TS L. major
Ligand CKP-41

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
11.8 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
99%
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.790 kcal/mol/HA) ✓ Good fit quality (FQ -7.90) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (99%) ✗ Moderate strain (11.8 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-26.847
kcal/mol
LE
-0.790
kcal/mol/HA
Fit Quality
-7.90
FQ (Leeson)
HAC
34
heavy atoms
MW
466
Da
LogP
7.02
cLogP
Strain ΔE
11.8 kcal/mol
SASA buried
82%
Lipo contact
99% BSA apolar/total
SASA unbound
785 Ų
Apolar buried
636 Ų

Interaction summary

HB 0 HY 24 PI 3 CLASH 0

HB · H-bonds
No hb · h-bonds detected for this pose.

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.
Final rank0.825Score-26.847
Inter norm-0.780Intra norm-0.010
Top1000noExcludedno
Contacts18H-bonds0
Artifact reasongeometry warning; 15 clashes
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 LEU94 MET53 PHE56 PHE91 PRO50 PRO88 THR180 TRP47 TYR162 VAL30 VAL31 VAL49 VAL87

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
Jaccard0.56RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
252 0.8246888350023713 -0.779717 -26.8469 0 18 14 0.67 0.00 - no Current
332 1.0812370356388297 -0.781349 -25.2373 0 20 0 0.00 0.00 - no Open
343 1.0920748065183272 -0.774106 -26.0899 0 17 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 -26.847kcal/mol
Ligand efficiency (LE) -0.7896kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.901
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 466.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 7.02
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 54.90kcal/mol
Minimised FF energy 43.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 784.9Ų
Total solvent-accessible surface area of free ligand
BSA total 640.3Ų
Buried surface area upon binding
BSA apolar 636.5Ų
Hydrophobic contacts buried
BSA polar 3.8Ų
Polar contacts buried
Fraction buried 81.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 99.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3509.3Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1696.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)