Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
15.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
43% of hydrophobic surface appears solvent-exposed (6/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.972 kcal/mol/HA)
✓ Good fit quality (FQ -8.29)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (15.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.420
kcal/mol
LE
-0.972
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
21
heavy atoms
MW
302
Da
LogP
2.65
cLogP
Final rank
2.4721
rank score
Inter norm
-1.188
normalised
Contacts
10
H-bonds 2
Interaction summary
HBA 2
HY 5
PI 5
CLASH 1
Interaction summary
HBA 2
HY 5
PI 5
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 528 | 2.124232310020372 | -1.22616 | -25.2086 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 2.131253891363639 | -1.27863 | -25.4778 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 481 | 2.213161850603409 | -1.23828 | -25.4847 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 170 | 2.246887908533105 | -1.23637 | -25.1405 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 163 | 2.275852750180273 | -1.26991 | -25.4586 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 126 | 2.3797589319540444 | -1.23414 | -25.3363 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 107 | 2.461393635290505 | -1.22589 | -21.5221 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 2.4720918578520474 | -1.18798 | -20.4201 | 2 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
| 464 | 4.648705661952587 | -1.41519 | -27.3298 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.420kcal/mol
Ligand efficiency (LE)
-0.9724kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.294
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
302.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.65
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
26.35kcal/mol
Minimised FF energy
11.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
548.0Ų
Total solvent-accessible surface area of free ligand
BSA total
467.9Ų
Buried surface area upon binding
BSA apolar
327.1Ų
Hydrophobic contacts buried
BSA polar
140.7Ų
Polar contacts buried
Fraction buried
85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1560.9Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1022.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)